Open sgiavasis opened 1 year ago
The gray regions in the image show the overlapping regions on the brain mask with and without the addition of the 2 transforms (motion correction and identity). As you can see from the image, the outputs do not change.
@tergeorge currently also running fmriprep on this data:
Current status:
Ran fmriprep-LTS and fmriprep 20.0.7 on lisa.
Run command:
/data3/cnl/mindboggle/opt/singularity/bin/singularity run -B /data3/cnl/tgeorge/Leonas_issue:/data3/cnl/tgeorge/Leonas_issue -B /data3/aki/Leona/cpac_output/sample_data_and_fmriprepoutput/BIDs-raw:/data3/aki/Leona/cpac_output/sample_data_and_fmriprepoutput/BIDs-raw -B /home/agutierrez/Documents/C-PAC/dev/docker_data --cleanenv /data3/cnl/tgeorge/Leonas_issue/images/fmriprep-20.2.7.sif /data3/aki/Leona/cpac_output/sample_data_and_fmriprepoutput/BIDs-raw /data3/cnl/tgeorge/Leonas_issue/output/fmriprep_LTS_sub-PA009 participant --participant-label sub-PA009 -t ovalfamily --skip-bids-validation --fd-spike-threshold 0.9 --dvars-spike-threshold 2.0 --bold2t1w-dof 12 --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --stop-on-first-crash --notrack -w /data3/cnl/tgeorge/Leonas_issue/work/fmriprep_LTS_sub-PA009 --skip_bids_validation --fs-license-file /home/agutierrez/Documents/C-PAC/dev/docker_data/license.txt --fs-no-reconall --nthreads 8 --omp-nthreads 8 --mem-mb 12000
Singularity image error:
Error message:
/data3/cnl/mindboggle/opt/singularity/bin/singularity run -B /data3/cnl/tgeorge/Leonas_issue:/data3/cnl/tgeorge/Leonas_issue -B /data3/aki/Leona/cpac_output/sample_data_and_fmriprepoutput/BIDs-raw:/data3/aki/Leona/cpac_output/sample_data_and_fmriprepoutput/BIDs-raw -B /home/agutierrez/Documents/C-PAC/dev/docker_data --cleanenv /data3/cnl/tgeorge/Leonas_issue/images/fmriprep-20.2.7.sif /data3/aki/Leona/cpac_output/sample_data_and_fmriprepoutput/BIDs-raw /data3/cnl/tgeorge/Leonas_issue/output/fmriprep_LTS_sub-PA009 participant --participant-label sub-PA009 -t ovalfamily --skip-bids-validation --fd-spike-threshold 0.9 --dvars-spike-threshold 2.0 --bold2t1w-dof 12 --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --stop-on-first-crash --notrack -w /data3/cnl/tgeorge/Leonas_issue/work/fmriprep_LTS_sub-PA009 --skip_bids_validation --fs-license-file /home/agutierrez/Documents/C-PAC/dev/docker_data/license.txt --fs-no-reconall --nthreads 8 --omp-nthreads 8 --mem-mb 12000
Next steps: Build the image on ACCESS and run fmriprep again with the new singularity images.
ACCESS run command:
LTS run:
singularity run --cleanenv /ocean/projects/med220004p/tgeorge/Leonas_issue/images/fmriprep_20.2.7.sif /ocean/projects/med220004p/tgeorge/Leonas_issue/input/BIDs-raw /ocean/projects/med220004p/tgeorge/Leonas_issue/output/fmriprep_LTS_sub-PA009 participant --participant-label sub-PA009 -t ovalfamily --skip-bids-validation --fd-spike-threshold 0.9 --dvars-spike-threshold 2.0 --bold2t1w-dof 12 --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --stop-on-first-crash --notrack -w /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_LTS_sub-PA009 --skip_bids_validation --fs-license-file /ocean/projects/med220004p/tgeorge/Leonas_issue/images/fs_license.txt --fs-no-reconall --nthreads 8 --omp-nthreads 8 --mem-mb 12000
fmrprep: 20.0.7
singularity run --cleanenv /ocean/projects/med220004p/tgeorge/Leonas_issue/images/fmriprep_20.0.7.sif /ocean/projects/med220004p/tgeorge/Leonas_issue/input/BIDs-raw /ocean/projects/med220004p/tgeorge/Leonas_issue/output/fmriprep_LTS_sub-PA009 participant --participant-label sub-PA009 -t ovalfamily --skip-bids-validation --fd-spike-threshold 0.9 --dvars-spike-threshold 2.0 --bold2t1w-dof 12 --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --stop-on-first-crash --notrack -w /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA009 --skip_bids_validation --fs-license-file /ocean/projects/med220004p/tgeorge/Leonas_issue/images/fs_license.txt --fs-no-reconall --nthreads 8 --omp-nthreads 8 --mem-mb 12000
Output dir of runs: /ocean/projects/med220004p/tgeorge/Leonas_issue/output
Working dir of runs: /ocean/projects/med220004p/tgeorge/Leonas_issue/work/
Fmriprep work directory outputs: https://docs.google.com/document/d/1k0O-IH-5ZmXM2EHhKg4v_BFatw4kKRduUQc5dPClGms/edit
Template space bold mask generation in fmriprep:
antsApplyTransforms --default-value 0 --float 1 --input /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_trans_corrected_brain_mask_maths_trans.nii.gz --reference-image /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_t1_trans_wf/gen_ref/sub-PA048_ses-V3W3_acq-MPR_rec-vNavNorm_T1w_corrected_masked_xform_reference.nii.gz --transform /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt
Template space bold mask generation in CPAC:
antsApplyTransforms --default-value 0 --float 0 --input /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/_scan_ovalfamily/combine_masks_112/ref_bold_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_brain_mask_maths_trans.nii.gz --reference-image /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/resampled_T1w-brain-template-funcreg/T1w-brain-template-funcreg/tpl-MNI152NLin2009cAsym_res-02_T1w_reference_resample.nii.gz --transform /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/ANTS_T1_to_template_58/write_composite_xfm/from-T1w_to-template_mode-image_xfm.nii.gz --transform /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/_scan_ovalfamily/convert_bbr2itk_200/affine.txt
Splitting these up:
fmriprep:
antsApplyTransforms
--default-value 0
--float 1
--input /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz
--interpolation MultiLabel
--output ref_bold_corrected_trans_corrected_brain_mask_maths_trans.nii.gz
--reference-image /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_t1_trans_wf/gen_ref/sub-PA048_ses-V3W3_acq-MPR_rec-vNavNorm_T1w_corrected_masked_xform_reference.nii.gz
--transform /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt
CPAC:
antsApplyTransforms
--default-value 0
--float 0
--input /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/_scan_ovalfamily/combine_masks_112/ref_bold_corrected_brain_mask_maths.nii.gz
--interpolation MultiLabel
--output ref_bold_corrected_brain_mask_maths_trans.nii.gz
--reference-image /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/resampled_T1w-brain-template-funcreg/T1w-brain-template-funcreg/tpl-MNI152NLin2009cAsym_res-02_T1w_reference_resample.nii.gz
--transform /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/ANTS_T1_to_template_58/write_composite_xfm/from-T1w_to-template_mode-image_xfm.nii.gz
--transform /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/_scan_ovalfamily/convert_bbr2itk_200/affine.txt
In the meantime-
Can we see an overlay of the two input files, plus a correlation of the two?
/ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz
vs.
/outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/_scan_ovalfamily/combine_masks_112/ref_bold_corrected_brain_mask_maths.nii.gz
And same with the two references?
/ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_t1_trans_wf/gen_ref/sub-PA048_ses-V3W3_acq-MPR_rec-vNavNorm_T1w_corrected_masked_xform_reference.nii.gz
vs.
/outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/resampled_T1w-brain-template-funcreg/T1w-brain-template-funcreg/tpl-MNI152NLin2009cAsym_res-02_T1w_reference_resample.nii.gz
This is what the two inputs look like:
The one on top with the multicolor border is from fmriprep. correlation of the input files: 0.945126
For the reference image, CPAC uses the whole head while fmriprep uses just the brain template. So I can't overlay the two. Also need to investigate why that is the case.
CPAC reference:
fmriprep reference:
These are the two outputs overlaid on top of each other. The green is the fmriprep output. As you can see both of them are pretty bad!!
The two outputs have a different dimensions. CPAC - [82x97x82] and fmriprep - [62x76x61].
--float 1
means that the output image should be stored as a floating point.
fmriprep:
antsApplyTransforms --default-value 0 --float 1 --input /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA009/fmriprep_wf/single_subject_PA009_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_brain_mask_maths_trans.nii.gz --reference-image /jet/home/tgeorge/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz --transform /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA009/fmriprep_wf/single_subject_PA009_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5 --transform /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA009/fmriprep_wf/single_subject_PA009_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt
Breaking up the command:
antsApplyTransforms
--default-value 0
--float 1
Input :
/ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA009/fmriprep_wf/single_subject_PA009_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz
ref:
/jet/home/tgeorge/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz
--interpolation MultiLabel
--transform /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA009/fmriprep_wf/single_subject_PA009_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
--transform /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA009/fmriprep_wf/single_subject_PA009_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt
The two inputs overlaid.
The one on top with the multicolor border is from fmriprep.
The two outputs overlaid:
The image with multicolor border is from fmriprep.
The two references:
Lucid chart flow diagram of the CPAC and fmriprep work flow. https://lucid.app/lucidchart/373d7542-1de0-4c12-bf84-7de997dd99a5/edit?invitationId=inv_277f6ed3-42da-4573-bb97-791bcb11cde6&page=0_0#
space-template_desc-bold_mask
produced by single-step resampling has some missing sections on the bottom, like it's clipped.sbref
.