refactor

[zswgzx]

Hi @gdevenyi , I'm not sure in what stage you'd like me to be involved, but I would like to send you my edited code (mostly minor changes). One function I think would help could be adding a function to generate the command(s) to run, which is included in the edited one I send. I hesitate to PR since I haven't run through the code locally or on cluster (I'll run the registration part on Azure cloud, if you're interested I can share how) . Which email works best for you? Thank you for your effort of building this wonder pipeline!

[gdevenyi]

Hi,

I welcome all PRs to the project. I just request that they be

1. One change per commit.
2. Documented clearly.
3. Tested.

With regards to:

a function to generate the command(s) to run

The --dry-run option should suffice there.

[zswgzx]

Could you provide the dry run output for an example run with 1level & 2level, respectively? It's hard to imagine the dry run result because I've refactored a lot including file naming, reducing to 600 lines or so.

[gdevenyi]

Here's a dry-run from a 2level run

twolevel_ants_dbm/twolevel_dbm.py \
  --dry-run \
  --rigid-model-target /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii \
  --modelbuild-command /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh \
  --cluster-type=slurm --walltime 8:00:00 2level /home/m/mchakrav/jgermann/scratch/dbm_ad/input.csv

twolevel_dbm.py: would run command: PrintHeader /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii 1
twolevel_dbm.py: Running 9 First-Level Modelbuilds
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject0/subject0_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3901-1_iN4_extr.nii input/3901-374_iN4_extr.nii && echo DONE > output/subject0/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject1/subject1_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3902-1_iN4_extr.nii input/3902-400_iN4_extr.nii && echo DONE > output/subject1/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject2/subject2_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3903-1_iN4_extr.nii input/3903-180_iN4_extr.nii input/3903-371_iN4_extr.nii && echo DONE > output/subject2/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject3/subject3_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3904-1_iN4_extr.nii input/3904-196_iN4_extr.nii input/3904-366_iN4_extr.nii && echo DONE > output/subject3/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject4/subject4_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3905-1_iN4_extr.nii input/3905-179_iN4_extr.nii input/3905-357_iN4_extr.nii && echo DONE > output/subject4/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject5/subject5_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3907-1_iN4_extr.nii input/3907-223_iN4_extr.nii input/3907-361_iN4_extr.nii && echo DONE > output/subject5/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject6/subject6_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3908-1_iN4_extr.nii input/3908-210_iN4_extr.nii && echo DONE > output/subject6/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject7/subject7_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3909-1_iN4_extr.nii input/3909-253_iN4_extr.nii input/3909-407_iN4_extr.nii && echo DONE > output/subject7/COMPLETE
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/subject8/subject8_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii input/3910-1_iN4_extr.nii input/3910-194_iN4_extr.nii input/3910-376_iN4_extr.nii && echo DONE > output/subject8/COMPLETE
twolevel_dbm.py: would run mkdir -p output/jacobians/overall
twolevel_dbm.py: would run mkdir -p output/compositewarps/secondlevel
twolevel_dbm.py: would run mkdir -p output/jacobians/common_space
twolevel_dbm.py: would run mkdir -p output/compositewarps/groupwise
twolevel_dbm.py: would run mkdir -p output/jacobians/resampled
twolevel_dbm.py: would run mkdir -p output/jacobians/groupwise
twolevel_dbm.py: would run mkdir -p output/jacobians/common_space/overall
twolevel_dbm.py: Running Second-Level Modelbuild
twolevel_dbm.py: would run command: /home/m/mchakrav/jgermann/scratch/dbm_ad/niagara2-antsMultivariateTemplateConstruction2.sh -d 3 -o output/secondlevel/secondlevel_ -r 1 -l 1 -y 0 -c 5 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 8:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 -z /home/m/mchakrav/jgermann/scratch/dbm_ad/mni_icbm152_t1_extracted_0.5mm.nii output/subject0/subject0_template0.nii.gz output/subject1/subject1_template0.nii.gz output/subject2/subject2_template0.nii.gz output/subject3/subject3_template0.nii.gz output/subject4/subject4_template0.nii.gz output/subject5/subject5_template0.nii.gz output/subject6/subject6_template0.nii.gz output/subject7/subject7_template0.nii.gz output/subject8/subject8_template0.nii.gz && echo DONE > output/secondlevel/COMPLETE
twolevel_dbm.py: would run command: ThresholdImage 3 output/secondlevel/secondlevel_template0.nii.gz output/secondlevel/secondlevel_otsumask.nii.gz Otsu 1
twolevel_dbm.py: Processing Second-Level DBM outputs
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject0_template001Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject0_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject0_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject0_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject0_template000GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject0_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject0_template001Warp.nii.gz output/jacobians/overall/secondlevel_subject0_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject0_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject0_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject0_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject0_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject1_template011Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject1_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject0_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject0_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject0_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject0_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject0_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject0_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject1_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject1_template0_delin.nii.gz,1]twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject1_template010GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject1_template0_affine.nii.gz,1]

twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject1_template011Warp.nii.gz output/jacobians/overall/secondlevel_subject1_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject1_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject1_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject1_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject1_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject2_template021Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject2_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject1_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject1_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject1_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject1_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject1_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject1_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject2_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject2_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject2_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject2_template021Warp.nii.gz output/jacobians/overall/secondlevel_subject2_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject2_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject2_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject2_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject2_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject3_template031Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject3_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject2_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject2_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject2_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject2_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject2_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject2_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject3_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject3_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject3_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject3_template031Warp.nii.gz output/jacobians/overall/secondlevel_subject3_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject3_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject3_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject3_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject3_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject4_template041Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject4_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject3_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject3_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject3_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject3_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject3_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject3_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject4_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject4_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject4_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject4_template041Warp.nii.gz output/jacobians/overall/secondlevel_subject4_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject4_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject4_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject4_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject4_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject5_template051Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject5_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject4_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject4_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject4_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject4_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject4_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject4_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject5_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject5_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject5_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject5_template051Warp.nii.gz output/jacobians/overall/secondlevel_subject5_template0_nlin.nii.gz 1 1twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject5_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject5_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject5_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject5_template0_affine.nii.gz 1 1

twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject6_template061Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject6_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject5_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject5_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject5_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject5_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject5_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject5_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject6_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject6_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject6_template060GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject6_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject6_template061Warp.nii.gz output/jacobians/overall/secondlevel_subject6_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject6_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject6_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject6_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject6_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject7_template071Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject7_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject6_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject6_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject6_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject6_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject6_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject6_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject7_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject7_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject7_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject7_template071Warp.nii.gz output/jacobians/overall/secondlevel_subject7_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject7_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject7_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject7_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject7_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/secondlevel/secondlevel_subject8_template081Warp.nii.gz 0.25 affine output/compositewarps/secondlevel/subject8_template0_delin.mat output/secondlevel/secondlevel_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject7_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject7_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject7_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject7_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject7_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject7_template0_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/secondlevel/subject8_template0_delin.mat,1] -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject8_template0_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o [output/compositewarps/secondlevel/subject8_template0_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/secondlevel/secondlevel_subject8_template081Warp.nii.gz output/jacobians/overall/secondlevel_subject8_template0_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject8_template0_delin.nii.gz output/jacobians/overall/secondlevel_subject8_template0_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/secondlevel/subject8_template0_affine.nii.gz output/jacobians/overall/secondlevel_subject8_template0_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject8_template0_relative.nii.gz + output/jacobians/overall/secondlevel_subject8_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject8_template0_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/secondlevel_subject8_template0_absolute.nii.gz + output/jacobians/overall/secondlevel_subject8_template0_nlin.nii.gz output/jacobians/overall/secondlevel_subject8_template0_affine.nii.gz
twolevel_dbm.py: would run command: echo DONE > output/compositewarps/secondlevel/COMPLETE
twolevel_dbm.py: Processing First-Level DBM Outputs
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject0/subject0_template0.nii.gz output/subject0/subject0_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject0/subject0_3901-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject0_3901-1_iN4_extr_delin.mat output/subject0/subject0_otsumask.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject0_3901-1_iN4_extr_delin.mat,1] -r output/subject0/subject0_template0.nii.gz -o [output/compositewarps/groupwise/subject0_3901-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject0/subject0_3901-1_iN4_extr00GenericAffine.mat -r output/subject0/subject0_template0.nii.gz -o [output/compositewarps/groupwise/subject0_3901-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject0/subject0_3901-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject0_3901-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject0_3901-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject0_3901-1_iN4_extr_delin.nii.gz 1 1twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject0_3901-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject0_3901-1_iN4_extr_affine.nii.gz 1 1

twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject0_3901-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject0_3901-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject0_3901-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject0_3901-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject0_3901-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject0_3901-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject0_3901-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject0_template001Warp.nii.gz -t output/secondlevel/secondlevel_subject0_template000GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject0_3901-1_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject0_3901-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject0_template001Warp.nii.gz -t output/secondlevel/secondlevel_subject0_template000GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject0_3901-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject0_3901-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject0_template001Warp.nii.gz -t output/secondlevel/secondlevel_subject0_template000GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject0_3901-1_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject0/subject0_3901-374_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject0_3901-374_iN4_extr_delin.mat output/subject0/subject0_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject0_3901-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject0_3901-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject0_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject0_3901-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject0_3901-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject0_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject0_3901-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject0_3901-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject0_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject0_3901-374_iN4_extr_delin.mat,1] -r output/subject0/subject0_template0.nii.gz -o [output/compositewarps/groupwise/subject0_3901-374_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject0/subject0_3901-374_iN4_extr10GenericAffine.mat -r output/subject0/subject0_template0.nii.gz -o [output/compositewarps/groupwise/subject0_3901-374_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject0/subject0_3901-374_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject0_3901-374_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject0_3901-374_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject0_3901-374_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject0_3901-374_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject0_3901-374_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject0_3901-374_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject0_3901-374_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject0_3901-374_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject0_3901-374_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject0_3901-374_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject0_3901-374_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject0_3901-374_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject0_template001Warp.nii.gz -t output/secondlevel/secondlevel_subject0_template000GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject0_3901-374_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject0_3901-374_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject0_template001Warp.nii.gz -t output/secondlevel/secondlevel_subject0_template000GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject0_3901-374_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject0_3901-374_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject0_template001Warp.nii.gz -t output/secondlevel/secondlevel_subject0_template000GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject0_3901-374_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject1/subject1_template0.nii.gz output/subject1/subject1_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject1/subject1_3902-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject1_3902-1_iN4_extr_delin.mat output/subject1/subject1_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject0_3901-374_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject0_3901-374_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject0_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject0_3901-374_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject0_3901-374_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject0_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject0_3901-374_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject0_3901-374_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject0_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject1_3902-1_iN4_extr_delin.mat,1] -r output/subject1/subject1_template0.nii.gz -o [output/compositewarps/groupwise/subject1_3902-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject1/subject1_3902-1_iN4_extr00GenericAffine.mat -r output/subject1/subject1_template0.nii.gz -o [output/compositewarps/groupwise/subject1_3902-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject1/subject1_3902-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject1_3902-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject1_3902-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject1_3902-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject1_3902-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject1_3902-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject1_3902-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject1_3902-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject1_3902-1_iN4_extr_delin.nii.gztwolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject1_3902-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject1_3902-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject1_3902-1_iN4_extr_affine.nii.gz

twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject1_3902-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject1_template011Warp.nii.gz -t output/secondlevel/secondlevel_subject1_template010GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject1_3902-1_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject1_3902-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject1_template011Warp.nii.gz -t output/secondlevel/secondlevel_subject1_template010GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject1_3902-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject1_3902-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject1_template011Warp.nii.gz -t output/secondlevel/secondlevel_subject1_template010GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject1_3902-1_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject1/subject1_3902-400_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject1_3902-400_iN4_extr_delin.mat output/subject1/subject1_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject1_3902-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject1_3902-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject1_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject1_3902-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject1_3902-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject1_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject1_3902-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject1_3902-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject1_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject1_3902-400_iN4_extr_delin.mat,1] -r output/subject1/subject1_template0.nii.gz -o [output/compositewarps/groupwise/subject1_3902-400_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject1/subject1_3902-400_iN4_extr10GenericAffine.mat -r output/subject1/subject1_template0.nii.gz -o [output/compositewarps/groupwise/subject1_3902-400_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject1/subject1_3902-400_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject1_3902-400_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject1_3902-400_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject1_3902-400_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject1_3902-400_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject1_3902-400_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject1_3902-400_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject1_3902-400_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject1_3902-400_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject1_3902-400_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject1_3902-400_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject1_3902-400_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject1_3902-400_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject1_template011Warp.nii.gz -t output/secondlevel/secondlevel_subject1_template010GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject1_3902-400_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject1_3902-400_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject1_template011Warp.nii.gz -t output/secondlevel/secondlevel_subject1_template010GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject1_3902-400_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject1_3902-400_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject1_template011Warp.nii.gz -t output/secondlevel/secondlevel_subject1_template010GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject1_3902-400_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject2/subject2_template0.nii.gz output/subject2/subject2_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject2/subject2_3903-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject2_3903-1_iN4_extr_delin.mat output/subject2/subject2_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject1_3902-400_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject1_3902-400_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject1_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject1_3902-400_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject1_3902-400_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject1_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject1_3902-400_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject1_3902-400_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject1_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject2_3903-1_iN4_extr_delin.mat,1] -r output/subject2/subject2_template0.nii.gz -o [output/compositewarps/groupwise/subject2_3903-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject2/subject2_3903-1_iN4_extr00GenericAffine.mat -r output/subject2/subject2_template0.nii.gz -o [output/compositewarps/groupwise/subject2_3903-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject2/subject2_3903-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject2_3903-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject2_3903-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject2_3903-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject2_3903-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject2_3903-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject2_3903-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject2_3903-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject2_3903-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject2_3903-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject2_3903-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject2_3903-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-1_iN4_extr_relative.nii.gztwolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-1_iN4_extr_nlin.nii.gz

twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject2/subject2_3903-180_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject2_3903-180_iN4_extr_delin.mat output/subject2/subject2_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject2_3903-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject2_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject2_3903-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject2_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject2_3903-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject2_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject2_3903-180_iN4_extr_delin.mat,1] -r output/subject2/subject2_template0.nii.gz -o [output/compositewarps/groupwise/subject2_3903-180_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject2/subject2_3903-180_iN4_extr10GenericAffine.mat -r output/subject2/subject2_template0.nii.gz -o [output/compositewarps/groupwise/subject2_3903-180_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject2/subject2_3903-180_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject2_3903-180_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject2_3903-180_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject2_3903-180_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject2_3903-180_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject2_3903-180_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject2_3903-180_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject2_3903-180_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject2_3903-180_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject2_3903-180_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject2_3903-180_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject2_3903-180_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-180_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-180_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-180_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-180_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-180_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-180_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject2/subject2_3903-371_iN4_extr21Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject2_3903-371_iN4_extr_delin.mat output/subject2/subject2_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-180_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject2_3903-180_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject2_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-180_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject2_3903-180_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject2_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-180_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject2_3903-180_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject2_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject2_3903-371_iN4_extr_delin.mat,1] -r output/subject2/subject2_template0.nii.gz -o [output/compositewarps/groupwise/subject2_3903-371_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject2/subject2_3903-371_iN4_extr20GenericAffine.mat -r output/subject2/subject2_template0.nii.gz -o [output/compositewarps/groupwise/subject2_3903-371_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject2/subject2_3903-371_iN4_extr21Warp.nii.gz output/jacobians/groupwise/subject2_3903-371_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject2_3903-371_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject2_3903-371_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject2_3903-371_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject2_3903-371_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject2_3903-371_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject2_3903-371_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject2_3903-371_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject2_3903-371_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject2_3903-371_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject2_3903-371_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-371_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-371_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-371_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-371_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject2_3903-371_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject2_template021Warp.nii.gz -t output/secondlevel/secondlevel_subject2_template020GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject2_3903-371_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject3/subject3_template0.nii.gz output/subject3/subject3_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject3/subject3_3904-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject3_3904-1_iN4_extr_delin.mat output/subject3/subject3_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-371_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject2_3903-371_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject2_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-371_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject2_3903-371_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject2_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject2_3903-371_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject2_3903-371_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject2_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject3_3904-1_iN4_extr_delin.mat,1] -r output/subject3/subject3_template0.nii.gz -o [output/compositewarps/groupwise/subject3_3904-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject3/subject3_3904-1_iN4_extr00GenericAffine.mat -r output/subject3/subject3_template0.nii.gz -o [output/compositewarps/groupwise/subject3_3904-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject3/subject3_3904-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject3_3904-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject3_3904-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject3_3904-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject3_3904-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject3_3904-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject3_3904-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject3_3904-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject3_3904-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject3_3904-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject3_3904-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject3_3904-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-1_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-1_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject3/subject3_3904-196_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject3_3904-196_iN4_extr_delin.mat output/subject3/subject3_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject3_3904-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject3_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject3_3904-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject3_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject3_3904-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject3_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject3_3904-196_iN4_extr_delin.mat,1] -r output/subject3/subject3_template0.nii.gz -o [output/compositewarps/groupwise/subject3_3904-196_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject3/subject3_3904-196_iN4_extr10GenericAffine.mat -r output/subject3/subject3_template0.nii.gz -o [output/compositewarps/groupwise/subject3_3904-196_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject3/subject3_3904-196_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject3_3904-196_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject3_3904-196_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject3_3904-196_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject3_3904-196_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject3_3904-196_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject3_3904-196_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject3_3904-196_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject3_3904-196_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject3_3904-196_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject3_3904-196_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject3_3904-196_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-196_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-196_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-196_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-196_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-196_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-196_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject3/subject3_3904-366_iN4_extr21Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject3_3904-366_iN4_extr_delin.mat output/subject3/subject3_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-196_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject3_3904-196_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject3_template0_relative.nii.gztwolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-196_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject3_3904-196_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject3_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-196_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject3_3904-196_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject3_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject3_3904-366_iN4_extr_delin.mat,1] -r output/subject3/subject3_template0.nii.gz -o [output/compositewarps/groupwise/subject3_3904-366_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject3/subject3_3904-366_iN4_extr20GenericAffine.mat -r output/subject3/subject3_template0.nii.gz -o [output/compositewarps/groupwise/subject3_3904-366_iN4_extr_affine.nii.gz,1]

twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject3/subject3_3904-366_iN4_extr21Warp.nii.gz output/jacobians/groupwise/subject3_3904-366_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject3_3904-366_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject3_3904-366_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject3_3904-366_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject3_3904-366_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject3_3904-366_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject3_3904-366_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject3_3904-366_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject3_3904-366_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject3_3904-366_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject3_3904-366_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-366_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-366_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-366_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-366_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject3_3904-366_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject3_template031Warp.nii.gz -t output/secondlevel/secondlevel_subject3_template030GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject3_3904-366_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject4/subject4_template0.nii.gz output/subject4/subject4_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject4/subject4_3905-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject4_3905-1_iN4_extr_delin.mat output/subject4/subject4_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-366_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject3_3904-366_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject3_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-366_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject3_3904-366_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject3_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject3_3904-366_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject3_3904-366_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject3_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject4_3905-1_iN4_extr_delin.mat,1] -r output/subject4/subject4_template0.nii.gz -o [output/compositewarps/groupwise/subject4_3905-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject4/subject4_3905-1_iN4_extr00GenericAffine.mat -r output/subject4/subject4_template0.nii.gz -o [output/compositewarps/groupwise/subject4_3905-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject4/subject4_3905-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject4_3905-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject4_3905-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject4_3905-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject4_3905-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject4_3905-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject4_3905-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject4_3905-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject4_3905-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject4_3905-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject4_3905-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject4_3905-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-1_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-1_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject4/subject4_3905-179_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject4_3905-179_iN4_extr_delin.mat output/subject4/subject4_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject4_3905-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject4_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject4_3905-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject4_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject4_3905-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject4_template0_nlin.nii.gztwolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject4_3905-179_iN4_extr_delin.mat,1] -r output/subject4/subject4_template0.nii.gz -o [output/compositewarps/groupwise/subject4_3905-179_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject4/subject4_3905-179_iN4_extr10GenericAffine.mat -r output/subject4/subject4_template0.nii.gz -o [output/compositewarps/groupwise/subject4_3905-179_iN4_extr_affine.nii.gz,1]

twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject4/subject4_3905-179_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject4_3905-179_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject4_3905-179_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject4_3905-179_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject4_3905-179_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject4_3905-179_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject4_3905-179_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject4_3905-179_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject4_3905-179_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject4_3905-179_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject4_3905-179_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject4_3905-179_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-179_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-179_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-179_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-179_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-179_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-179_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject4/subject4_3905-357_iN4_extr21Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject4_3905-357_iN4_extr_delin.mat output/subject4/subject4_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-179_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject4_3905-179_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject4_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-179_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject4_3905-179_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject4_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-179_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject4_3905-179_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject4_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject4_3905-357_iN4_extr_delin.mat,1] -r output/subject4/subject4_template0.nii.gz -o [output/compositewarps/groupwise/subject4_3905-357_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject4/subject4_3905-357_iN4_extr20GenericAffine.mat -r output/subject4/subject4_template0.nii.gz -o [output/compositewarps/groupwise/subject4_3905-357_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject4/subject4_3905-357_iN4_extr21Warp.nii.gz output/jacobians/groupwise/subject4_3905-357_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject4_3905-357_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject4_3905-357_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject4_3905-357_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject4_3905-357_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject4_3905-357_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject4_3905-357_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject4_3905-357_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject4_3905-357_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject4_3905-357_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject4_3905-357_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-357_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-357_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-357_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-357_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject4_3905-357_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject4_template041Warp.nii.gz -t output/secondlevel/secondlevel_subject4_template040GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject4_3905-357_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject5/subject5_template0.nii.gz output/subject5/subject5_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject5/subject5_3907-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject5_3907-1_iN4_extr_delin.mat output/subject5/subject5_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-357_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject4_3905-357_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject4_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-357_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject4_3905-357_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject4_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject4_3905-357_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject4_3905-357_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject4_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject5_3907-1_iN4_extr_delin.mat,1] -r output/subject5/subject5_template0.nii.gz -o [output/compositewarps/groupwise/subject5_3907-1_iN4_extr_delin.nii.gz,1]twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject5/subject5_3907-1_iN4_extr00GenericAffine.mat -r output/subject5/subject5_template0.nii.gz -o [output/compositewarps/groupwise/subject5_3907-1_iN4_extr_affine.nii.gz,1]

twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject5/subject5_3907-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject5_3907-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject5_3907-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject5_3907-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject5_3907-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject5_3907-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject5_3907-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject5_3907-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject5_3907-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject5_3907-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject5_3907-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject5_3907-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-1_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-1_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject5/subject5_3907-223_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject5_3907-223_iN4_extr_delin.mat output/subject5/subject5_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject5_3907-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject5_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject5_3907-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject5_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject5_3907-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject5_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject5_3907-223_iN4_extr_delin.mat,1] -r output/subject5/subject5_template0.nii.gz -o [output/compositewarps/groupwise/subject5_3907-223_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject5/subject5_3907-223_iN4_extr10GenericAffine.mat -r output/subject5/subject5_template0.nii.gz -o [output/compositewarps/groupwise/subject5_3907-223_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject5/subject5_3907-223_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject5_3907-223_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject5_3907-223_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject5_3907-223_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject5_3907-223_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject5_3907-223_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject5_3907-223_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject5_3907-223_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject5_3907-223_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject5_3907-223_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject5_3907-223_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject5_3907-223_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-223_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-223_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-223_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-223_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-223_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-223_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject5/subject5_3907-361_iN4_extr21Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject5_3907-361_iN4_extr_delin.mat output/subject5/subject5_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-223_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject5_3907-223_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject5_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-223_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject5_3907-223_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject5_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-223_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject5_3907-223_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject5_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject5_3907-361_iN4_extr_delin.mat,1] -r output/subject5/subject5_template0.nii.gz -o [output/compositewarps/groupwise/subject5_3907-361_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject5/subject5_3907-361_iN4_extr20GenericAffine.mat -r output/subject5/subject5_template0.nii.gz -o [output/compositewarps/groupwise/subject5_3907-361_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject5/subject5_3907-361_iN4_extr21Warp.nii.gz output/jacobians/groupwise/subject5_3907-361_iN4_extr_nlin.nii.gz 1 1twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject5_3907-361_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject5_3907-361_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject5_3907-361_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject5_3907-361_iN4_extr_affine.nii.gz 1 1

twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject5_3907-361_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject5_3907-361_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject5_3907-361_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject5_3907-361_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject5_3907-361_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject5_3907-361_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-361_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-361_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-361_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-361_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject5_3907-361_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject5_template051Warp.nii.gz -t output/secondlevel/secondlevel_subject5_template050GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject5_3907-361_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject6/subject6_template0.nii.gz output/subject6/subject6_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject6/subject6_3908-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject6_3908-1_iN4_extr_delin.mat output/subject6/subject6_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-361_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject5_3907-361_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject5_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-361_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject5_3907-361_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject5_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject5_3907-361_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject5_3907-361_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject5_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject6_3908-1_iN4_extr_delin.mat,1] -r output/subject6/subject6_template0.nii.gz -o [output/compositewarps/groupwise/subject6_3908-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject6/subject6_3908-1_iN4_extr00GenericAffine.mat -r output/subject6/subject6_template0.nii.gz -o [output/compositewarps/groupwise/subject6_3908-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject6/subject6_3908-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject6_3908-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject6_3908-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject6_3908-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject6_3908-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject6_3908-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject6_3908-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject6_3908-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject6_3908-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject6_3908-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject6_3908-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject6_3908-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject6_3908-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject6_template061Warp.nii.gz -t output/secondlevel/secondlevel_subject6_template060GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject6_3908-1_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject6_3908-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject6_template061Warp.nii.gz -t output/secondlevel/secondlevel_subject6_template060GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject6_3908-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject6_3908-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject6_template061Warp.nii.gz -t output/secondlevel/secondlevel_subject6_template060GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject6_3908-1_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject6/subject6_3908-210_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject6_3908-210_iN4_extr_delin.mat output/subject6/subject6_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject6_3908-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject6_3908-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject6_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject6_3908-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject6_3908-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject6_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject6_3908-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject6_3908-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject6_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject6_3908-210_iN4_extr_delin.mat,1] -r output/subject6/subject6_template0.nii.gz -o [output/compositewarps/groupwise/subject6_3908-210_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject6/subject6_3908-210_iN4_extr10GenericAffine.mat -r output/subject6/subject6_template0.nii.gz -o [output/compositewarps/groupwise/subject6_3908-210_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject6/subject6_3908-210_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject6_3908-210_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject6_3908-210_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject6_3908-210_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject6_3908-210_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject6_3908-210_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject6_3908-210_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject6_3908-210_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject6_3908-210_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject6_3908-210_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject6_3908-210_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject6_3908-210_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject6_3908-210_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject6_template061Warp.nii.gz -t output/secondlevel/secondlevel_subject6_template060GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject6_3908-210_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject6_3908-210_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject6_template061Warp.nii.gz -t output/secondlevel/secondlevel_subject6_template060GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject6_3908-210_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject6_3908-210_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject6_template061Warp.nii.gz -t output/secondlevel/secondlevel_subject6_template060GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject6_3908-210_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject6_3908-210_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject6_3908-210_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject6_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject6_3908-210_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject6_3908-210_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject6_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject6_3908-210_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject6_3908-210_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject6_template0_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject7/subject7_template0.nii.gz output/subject7/subject7_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject7/subject7_3909-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject7_3909-1_iN4_extr_delin.mat output/subject7/subject7_otsumask.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject7_3909-1_iN4_extr_delin.mat,1] -r output/subject7/subject7_template0.nii.gz -o [output/compositewarps/groupwise/subject7_3909-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject7/subject7_3909-1_iN4_extr00GenericAffine.mat -r output/subject7/subject7_template0.nii.gz -o [output/compositewarps/groupwise/subject7_3909-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject7/subject7_3909-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject7_3909-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject7_3909-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject7_3909-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject7_3909-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject7_3909-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject7_3909-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject7_3909-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject7_3909-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject7_3909-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject7_3909-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject7_3909-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-1_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-1_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject7/subject7_3909-253_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject7_3909-253_iN4_extr_delin.mat output/subject7/subject7_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject7_3909-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject7_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject7_3909-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject7_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject7_3909-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject7_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject7_3909-253_iN4_extr_delin.mat,1] -r output/subject7/subject7_template0.nii.gz -o [output/compositewarps/groupwise/subject7_3909-253_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject7/subject7_3909-253_iN4_extr10GenericAffine.mat -r output/subject7/subject7_template0.nii.gz -o [output/compositewarps/groupwise/subject7_3909-253_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject7/subject7_3909-253_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject7_3909-253_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject7_3909-253_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject7_3909-253_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject7_3909-253_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject7_3909-253_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject7_3909-253_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject7_3909-253_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject7_3909-253_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject7_3909-253_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject7_3909-253_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject7_3909-253_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-253_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-253_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-253_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-253_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-253_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-253_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject7/subject7_3909-407_iN4_extr21Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject7_3909-407_iN4_extr_delin.mat output/subject7/subject7_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-253_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject7_3909-253_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject7_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-253_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject7_3909-253_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject7_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-253_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject7_3909-253_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject7_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject7_3909-407_iN4_extr_delin.mat,1] -r output/subject7/subject7_template0.nii.gz -o [output/compositewarps/groupwise/subject7_3909-407_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject7/subject7_3909-407_iN4_extr20GenericAffine.mat -r output/subject7/subject7_template0.nii.gz -o [output/compositewarps/groupwise/subject7_3909-407_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject7/subject7_3909-407_iN4_extr21Warp.nii.gz output/jacobians/groupwise/subject7_3909-407_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject7_3909-407_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject7_3909-407_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject7_3909-407_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject7_3909-407_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject7_3909-407_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject7_3909-407_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject7_3909-407_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject7_3909-407_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject7_3909-407_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject7_3909-407_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-407_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-407_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-407_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-407_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject7_3909-407_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject7_template071Warp.nii.gz -t output/secondlevel/secondlevel_subject7_template070GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject7_3909-407_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ThresholdImage 3 output/subject8/subject8_template0.nii.gz output/subject8/subject8_otsumask.nii.gz Otsu 1
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject8/subject8_3910-1_iN4_extr01Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject8_3910-1_iN4_extr_delin.mat output/subject8/subject8_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-407_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject7_3909-407_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject7_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-407_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject7_3909-407_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject7_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject7_3909-407_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject7_3909-407_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject7_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject8_3910-1_iN4_extr_delin.mat,1] -r output/subject8/subject8_template0.nii.gz -o [output/compositewarps/groupwise/subject8_3910-1_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject8/subject8_3910-1_iN4_extr00GenericAffine.mat -r output/subject8/subject8_template0.nii.gz -o [output/compositewarps/groupwise/subject8_3910-1_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject8/subject8_3910-1_iN4_extr01Warp.nii.gz output/jacobians/groupwise/subject8_3910-1_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject8_3910-1_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject8_3910-1_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject8_3910-1_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject8_3910-1_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject8_3910-1_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject8_3910-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject8_3910-1_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject8_3910-1_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject8_3910-1_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject8_3910-1_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-1_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-1_iN4_extr_relative.nii.gztwolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-1_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-1_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-1_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-1_iN4_extr_nlin.nii.gz

twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject8/subject8_3910-194_iN4_extr11Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject8_3910-194_iN4_extr_delin.mat output/subject8/subject8_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-1_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject8_3910-1_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject8_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-1_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject8_3910-1_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject8_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-1_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject8_3910-1_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject8_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject8_3910-194_iN4_extr_delin.mat,1] -r output/subject8/subject8_template0.nii.gz -o [output/compositewarps/groupwise/subject8_3910-194_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject8/subject8_3910-194_iN4_extr10GenericAffine.mat -r output/subject8/subject8_template0.nii.gz -o [output/compositewarps/groupwise/subject8_3910-194_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject8/subject8_3910-194_iN4_extr11Warp.nii.gz output/jacobians/groupwise/subject8_3910-194_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject8_3910-194_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject8_3910-194_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject8_3910-194_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject8_3910-194_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject8_3910-194_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject8_3910-194_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject8_3910-194_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject8_3910-194_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject8_3910-194_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject8_3910-194_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-194_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-194_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-194_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-194_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-194_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-194_iN4_extr_nlin.nii.gz
twolevel_dbm.py: would run command: ANTSUseDeformationFieldToGetAffineTransform output/subject8/subject8_3910-376_iN4_extr21Warp.nii.gz 0.25 affine output/compositewarps/groupwise/subject8_3910-376_iN4_extr_delin.mat output/subject8/subject8_otsumask.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-194_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject8_3910-194_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject8_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-194_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject8_3910-194_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject8_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-194_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject8_3910-194_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject8_template0_nlin.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t [output/compositewarps/groupwise/subject8_3910-376_iN4_extr_delin.mat,1] -r output/subject8/subject8_template0.nii.gz -o [output/compositewarps/groupwise/subject8_3910-376_iN4_extr_delin.nii.gz,1]
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -t output/subject8/subject8_3910-376_iN4_extr20GenericAffine.mat -r output/subject8/subject8_template0.nii.gz -o [output/compositewarps/groupwise/subject8_3910-376_iN4_extr_affine.nii.gz,1]
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/subject8/subject8_3910-376_iN4_extr21Warp.nii.gz output/jacobians/groupwise/subject8_3910-376_iN4_extr_nlin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject8_3910-376_iN4_extr_delin.nii.gz output/jacobians/groupwise/subject8_3910-376_iN4_extr_delin.nii.gz 1 1
twolevel_dbm.py: would run command: CreateJacobianDeterminantImage 3 output/compositewarps/groupwise/subject8_3910-376_iN4_extr_affine.nii.gz output/jacobians/groupwise/subject8_3910-376_iN4_extr_affine.nii.gz 1 1
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject8_3910-376_iN4_extr_relative.nii.gz + output/jacobians/groupwise/subject8_3910-376_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject8_3910-376_iN4_extr_delin.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/groupwise/subject8_3910-376_iN4_extr_absolute.nii.gz + output/jacobians/groupwise/subject8_3910-376_iN4_extr_nlin.nii.gz output/jacobians/groupwise/subject8_3910-376_iN4_extr_affine.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-376_iN4_extr_relative.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-376_iN4_extr_relative.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-376_iN4_extr_absolute.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-376_iN4_extr_absolute.nii.gz
twolevel_dbm.py: would run command: antsApplyTransforms -d 3 --verbose -i output/jacobians/groupwise/subject8_3910-376_iN4_extr_nlin.nii.gz -t output/secondlevel/secondlevel_subject8_template081Warp.nii.gz -t output/secondlevel/secondlevel_subject8_template080GenericAffine.mat -r output/secondlevel/secondlevel_template0.nii.gz -o output/jacobians/resampled/subject8_3910-376_iN4_extr_nlin.nii.gz
twolevel_dbm.py: Blurring Jacobians
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-376_iN4_extr_relative.nii.gz + output/jacobians/resampled/subject8_3910-376_iN4_extr_relative.nii.gz output/jacobians/overall/secondlevel_subject8_template0_relative.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-376_iN4_extr_absolute.nii.gz + output/jacobians/resampled/subject8_3910-376_iN4_extr_absolute.nii.gz output/jacobians/overall/secondlevel_subject8_template0_absolute.nii.gz
twolevel_dbm.py: would run command: ImageMath 3 output/jacobians/overall/subject8_3910-376_iN4_extr_nlin.nii.gz + output/jacobians/resampled/subject8_3910-376_iN4_extr_nlin.nii.gz output/jacobians/overall/secondlevel_subject8_template0_nlin.nii.gz
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject0_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject0_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject0_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject0_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject0_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject0_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject1_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject1_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject1_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject1_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject1_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject1_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject2_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject2_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject2_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject2_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject2_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject2_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject3_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject3_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject3_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject3_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject3_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject3_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject4_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject4_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject4_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject4_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject4_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject4_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject5_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject5_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject5_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject5_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject5_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject5_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject6_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject6_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject6_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject6_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject6_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject6_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject7_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject7_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject7_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject7_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject7_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject7_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject8_template0_relative.nii.gz 0 output/jacobians/overall/secondlevel_subject8_template0_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject8_template0_absolute.nii.gz 0 output/jacobians/overall/secondlevel_subject8_template0_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/secondlevel_subject8_template0_nlin.nii.gz 0 output/jacobians/overall/secondlevel_subject8_template0_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject0_3901-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject0_3901-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject0_3901-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject0_3901-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject0_3901-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject0_3901-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject0_3901-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject0_3901-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject0_3901-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject0_3901-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject0_3901-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject0_3901-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject0_3901-374_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject0_3901-374_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject0_3901-374_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject0_3901-374_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject0_3901-374_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject0_3901-374_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject0_3901-374_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject0_3901-374_iN4_extr_relative_smooth0.nii.gz 1 0twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject0_3901-374_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject0_3901-374_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject0_3901-374_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject0_3901-374_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject1_3902-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject1_3902-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject1_3902-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject1_3902-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject1_3902-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject1_3902-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject1_3902-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject1_3902-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject1_3902-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject1_3902-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject1_3902-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject1_3902-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject1_3902-400_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject1_3902-400_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject1_3902-400_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject1_3902-400_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject1_3902-400_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject1_3902-400_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject1_3902-400_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject1_3902-400_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject1_3902-400_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject1_3902-400_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject1_3902-400_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject1_3902-400_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject2_3903-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject2_3903-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject2_3903-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject2_3903-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject2_3903-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject2_3903-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-180_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject2_3903-180_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-180_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject2_3903-180_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-180_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject2_3903-180_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-180_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject2_3903-180_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-180_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject2_3903-180_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-180_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject2_3903-180_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-371_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject2_3903-371_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-371_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject2_3903-371_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject2_3903-371_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject2_3903-371_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-371_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject2_3903-371_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-371_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject2_3903-371_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject2_3903-371_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject2_3903-371_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject3_3904-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject3_3904-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject3_3904-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject3_3904-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject3_3904-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject3_3904-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-196_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject3_3904-196_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-196_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject3_3904-196_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-196_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject3_3904-196_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-196_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject3_3904-196_iN4_extr_relative_smooth0.nii.gz 1 0twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-196_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject3_3904-196_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-196_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject3_3904-196_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-366_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject3_3904-366_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-366_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject3_3904-366_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject3_3904-366_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject3_3904-366_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-366_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject3_3904-366_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-366_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject3_3904-366_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject3_3904-366_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject3_3904-366_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject4_3905-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject4_3905-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject4_3905-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject4_3905-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject4_3905-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject4_3905-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-179_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject4_3905-179_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-179_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject4_3905-179_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-179_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject4_3905-179_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-179_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject4_3905-179_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-179_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject4_3905-179_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-179_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject4_3905-179_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-357_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject4_3905-357_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-357_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject4_3905-357_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject4_3905-357_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject4_3905-357_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-357_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject4_3905-357_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-357_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject4_3905-357_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject4_3905-357_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject4_3905-357_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject5_3907-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject5_3907-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject5_3907-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject5_3907-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject5_3907-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject5_3907-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-223_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject5_3907-223_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-223_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject5_3907-223_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-223_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject5_3907-223_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-223_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject5_3907-223_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-223_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject5_3907-223_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-223_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject5_3907-223_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-361_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject5_3907-361_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-361_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject5_3907-361_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject5_3907-361_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject5_3907-361_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-361_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject5_3907-361_iN4_extr_relative_smooth0.nii.gz 1 0twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-361_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject5_3907-361_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject5_3907-361_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject5_3907-361_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject6_3908-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject6_3908-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject6_3908-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject6_3908-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject6_3908-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject6_3908-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject6_3908-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject6_3908-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject6_3908-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject6_3908-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject6_3908-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject6_3908-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject6_3908-210_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject6_3908-210_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject6_3908-210_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject6_3908-210_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject6_3908-210_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject6_3908-210_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject6_3908-210_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject6_3908-210_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject6_3908-210_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject6_3908-210_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject6_3908-210_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject6_3908-210_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject7_3909-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject7_3909-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject7_3909-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject7_3909-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject7_3909-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject7_3909-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-253_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject7_3909-253_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-253_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject7_3909-253_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-253_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject7_3909-253_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-253_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject7_3909-253_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-253_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject7_3909-253_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-253_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject7_3909-253_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-407_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject7_3909-407_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-407_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject7_3909-407_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject7_3909-407_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject7_3909-407_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-407_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject7_3909-407_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-407_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject7_3909-407_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject7_3909-407_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject7_3909-407_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-1_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject8_3910-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-1_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject8_3910-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-1_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject8_3910-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-1_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject8_3910-1_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-1_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject8_3910-1_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-1_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject8_3910-1_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-194_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject8_3910-194_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-194_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject8_3910-194_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-194_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject8_3910-194_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-194_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject8_3910-194_iN4_extr_relative_smooth0.nii.gz 1 0twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-194_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject8_3910-194_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-194_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject8_3910-194_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-376_iN4_extr_relative.nii.gz 0 output/jacobians/resampled/subject8_3910-376_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-376_iN4_extr_absolute.nii.gz 0 output/jacobians/resampled/subject8_3910-376_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/resampled/subject8_3910-376_iN4_extr_nlin.nii.gz 0 output/jacobians/resampled/subject8_3910-376_iN4_extr_nlin_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-376_iN4_extr_relative.nii.gz 0 output/jacobians/overall/subject8_3910-376_iN4_extr_relative_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-376_iN4_extr_absolute.nii.gz 0 output/jacobians/overall/subject8_3910-376_iN4_extr_absolute_smooth0.nii.gz 1 0
twolevel_dbm.py: would run command: SmoothImage 3 output/jacobians/overall/subject8_3910-376_iN4_extr_nlin.nii.gz 0 output/jacobians/overall/subject8_3910-376_iN4_extr_nlin_smooth0.nii.gz 1 0

twolevel_dbm.py: would run command: echo DONE > output/jacobians/resampled/COMPLETE
twolevel_dbm.py: Pipeline Complete

[zswgzx]

Thanks, I'm running two scans for 1level (I changed the name to avoid confusion of my edits):

python 2level.py --cluster-type local -j 4 --resample-to-common-space template.nii.gz 1level input-l1.csv

where:

$ cat input-l1.csv
input/288739/tp1.nii.gz
input/268113/tp1.nii.gz

I'll based on the folder structure as above just for convenience.

What I wonder is how -j should be chosen. I used 4 since I have a 8-core machine, but ants seems to run with all occupied so it's somewhat slow. Maybe I confuse threads and cores. Could you advise?

[gdevenyi]

--local-threads only affects the parallelism for post-processing.

For the modelbuild side, antsRegistration uses all available threads and the ANTs scripts haven't really exposed the ability to limit that. --cluster-type local limits the modelbuild to only running a single antsRegistration at a time however.

[zswgzx]

I've refactored the first_level part but would like your help with the results part (i.e. line 239 in current code).

How should I convert subj_id and visit in the similar line below? I decided that the inputs are "input/[subj_id]/[visit].nii.gz". User can easily use "ln -s [src] input/..." to build the input folder structure so that the need to parse user specific path can be skipped. Please let me know what you think.

first_level

``` def first_level(inputs, args): cmds, images, results = list(), list(), list() for subject in inputs: # determine subj_id and visit # TODO: check if inputs follow path pattern "input/[subj_id]/[visit].nii.gz,..." subj_id = PurePath(str(subject)).parents[0].name visit = PurePath(str(subject)).name.rsplit(image_ext)[0] if not is_non_zero_file(f"output/{subj_id}/COMPLETE"): if len(subject) == 1: # cross section? command = f"mkdir -p output/{subj_id} && cp -p {subject[0]} output/{subj_id}/template0.nii.gz \ && ImageMath 3 output/{subj_id}/0-0GenericAffine.mat MakeAffineTransform 1 \ && CreateImage 3 {subject[0]} output/{subj_id}/0-1Warp.nii.gz 1 \ && CreateDisplacementField 3 1 " command += f"output/{subj_id}/0-1Warp.nii.gz " * 3 + \ f"output/{subj_id}/0-1InverseWarp.nii.gz && CreateDisplacementField 3 1 " + \ f"output/{subj_id}/0-1Warp.nii.gz " * 4 else: # Base command, default: bootstrap model builds with rigid pre-alignment w/o update command = f"{args.modelbuild_command} -d 3 -i {args.model_iterations} -o output/{subj_id}/{visit}_ \ -a {args.average_type} -e {args.float} -f {args.reg_shrinks} -g {args.gradient_step} \ -m {args.metric} -n {int(args.N4)} -q {args.reg_iterations} -r 1 -s {args.reg_smoothing} \ -t {args.transform} -y 0 \ -c {args.cluster_type} -u {args.walltime} -v {args.memory_request}" if args.rigid_model_target: command += f"-z {args.rigid_model_target} " command += " ".join(subject) command += f" && echo DONE > output/{subj_id}/COMPLETE" cmds.append(command) images.append(subject + f" output/{subj_id}/template0.nii.gz") # TODO: add the ability to limit the number of commands submitted if len(cmds): pool = threading.ThreadPool(nodes=args.local_threads) print(f"{script_name}: Running {len(cmds)} Level1 Model builds") for item in tqdm.tqdm(pool.uimap(lambda x: run_command(x, args.dry_run, args.verbose), cmds), total=len(cmds)): results.append(item) if not args.dry_run: for i, result in enumerate(results): subj_id = visit = with open(f"output/{subj_id}/{visit}.log", "wb") as l1_log: l1_log.write(cmds[i].encode()) l1_log.write(result.stdout) # Completely destroy the pool so that pathos doesn't reuse pool.close() pool.clear() second_level(images, args, bool(1)) ```

[gdevenyi]

Hi.

I'm not sure where you're going with this right now. Why don't you open a Draft PR to show whats been done so far so we can do a proper code review and discuss the changes and potential future changes.

[zswgzx]

re-running the following with 4x4x4mm input images:

python 2level.py --no-N4 --float --resample-to-common-space template.nii.gz -v 1level input-l1.csv

where

$ cat input-l1.csv 
input/288739/1.nii.gz
input/268113/1.nii.gz

But the following messages showed:

twolevel_dbm.py: running command: SmoothImage 3 output/jacobians/common_space/secondlevel_1_nlin.nii.gz 3.3972872011520763 output/jacobians/common_space/secondlevel_1_nlin_smooth3.3972872011520763.nii.gz 1 0
100%|█████████████████████████████████████████████████| 12/12 [00:01<00:00,  9.43it/s]
Using double precision for computations.
Input scalar image: output/jacobians/overall/secondlevel_1_relative.nii.gz
 file output/jacobians/overall/secondlevel_1_relative.nii.gz does not exist . 
Reference image: template.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. output/secondlevel/template0_common_space_0GenericAffine.mat (type = AffineTransform)
  2. output/secondlevel/template0_common_space_1Warp.nii.gz (type = DisplacementFieldTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /home/shengwei/work/software/antsBuild/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1322:
itk::ERROR: ResampleImageFilter(0x337e370): Input Primary is required but not set.
Aborted (core dumped)

Exception caught during reference file reading 

itk::ExceptionObject (0x25a8d40)
Location: "unknown" 
File: /home/shengwei/work/software/antsBuild/ITKv5/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx
Line: 562
Description: itk::ERROR: NiftiImageIO(0x25adc30): nifti_image_read (just header) failed for file: output/jacobians/overall/secondlevel_1_delin.nii.gz

 file output/jacobians/overall/secondlevel_1_delin.nii.gz
Segmentation fault (core dumped)

Any thoughts? Thank you!

[gdevenyi]

$ cat input-l1.csv 
input/288739/1.nii.gz
input/268113/1.nii.gz

As the file name of each input file is used in a flat directory structure, you cannot use the same filename for multiple inputs.