Path with dots breaks `antsMultivariateTemplateConstruction2.sh`

njhunsak commented 2 years ago

I've installed this pipeline and was attempting to verify the installation was done correctly. Here's the output when I ran the pipeline_test.sh. The program antsMultivariateTemplateConstruction2_fixed_random_seed.sh is looking for a directory, selection, that does not exist. Do I need to include more information when I run ./pipeline_test.sh?

output log

``` (harmonization) tests $ ./pipeline_test.sh connectom_prisma/ connectom_prisma/connectom/ connectom_prisma/connectom/A/ connectom_prisma/connectom/A/dwi_A_connectom_st_b1200.bval connectom_prisma/connectom/A/dwi_A_connectom_st_b1200.bvec connectom_prisma/connectom/A/dwi_A_connectom_st_b1200_mask.nii.gz connectom_prisma/connectom/A/dwi_A_connectom_st_b1200.nii.gz connectom_prisma/connectom/B/ connectom_prisma/connectom/B/dwi_B_connectom_st_b1200.bval connectom_prisma/connectom/B/dwi_B_connectom_st_b1200.bvec connectom_prisma/connectom/B/dwi_B_connectom_st_b1200_mask.nii.gz connectom_prisma/connectom/B/dwi_B_connectom_st_b1200.nii.gz connectom_prisma/connectom/C/ connectom_prisma/connectom/C/dwi_C_connectom_st_b1200.bval connectom_prisma/connectom/C/dwi_C_connectom_st_b1200.bvec connectom_prisma/connectom/C/dwi_C_connectom_st_b1200_mask.nii.gz connectom_prisma/connectom/C/dwi_C_connectom_st_b1200.nii.gz connectom_prisma/prisma/ connectom_prisma/prisma/A/ connectom_prisma/prisma/A/dwi_A_prisma_st_b1200.bval connectom_prisma/prisma/A/dwi_A_prisma_st_b1200.bvec connectom_prisma/prisma/A/dwi_A_prisma_st_b1200_mask.nii.gz connectom_prisma/prisma/A/dwi_A_prisma_st_b1200.nii.gz connectom_prisma/prisma/B/ connectom_prisma/prisma/B/dwi_B_prisma_st_b1200.bval connectom_prisma/prisma/B/dwi_B_prisma_st_b1200.bvec connectom_prisma/prisma/B/dwi_B_prisma_st_b1200_mask.nii.gz connectom_prisma/prisma/B/dwi_B_prisma_st_b1200.nii.gz connectom_prisma/prisma/C/ connectom_prisma/prisma/C/dwi_C_prisma_st_b1200.bval connectom_prisma/prisma/C/dwi_C_prisma_st_b1200.bvec connectom_prisma/prisma/C/dwi_C_prisma_st_b1200_mask.nii.gz connectom_prisma/prisma/C/dwi_C_prisma_st_b1200.nii.gz connectom_prisma/connectom.txt connectom_prisma/prisma.txt Determining maximum possible order of spherical harmonics for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dwi_A_connectom_st_b1200.bval Maximum possible order is 2 for 13 non-zero gradients Verifying /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dwi_A_connectom_st_b1200.bval is single shell ... b-shell bvalues [ 0. 1200.] Indices corresponding to b-shell 0.0 [ 0 8 15] Indices corresponding to b-shell 1200.0 [ 1 2 3 4 5 6 7 9 10 11 12 13 14] Verifying suitability of spherical harmonics order 2 for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dwi_A_connectom_st_b1200.bval Determining maximum possible order of spherical harmonics for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dwi_A_connectom_st_b1200.bval Maximum possible order is 2 for 13 non-zero gradients Spherical harmonics order 2 is suitable, continuing Verifying /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/dwi_B_connectom_st_b1200.bval is single shell ... b-shell bvalues [ 0. 1200.] Indices corresponding to b-shell 0.0 [ 0 8 15] Indices corresponding to b-shell 1200.0 [ 1 2 3 4 5 6 7 9 10 11 12 13 14] Verifying suitability of spherical harmonics order 2 for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/dwi_B_connectom_st_b1200.bval Determining maximum possible order of spherical harmonics for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/dwi_B_connectom_st_b1200.bval Maximum possible order is 2 for 13 non-zero gradients Spherical harmonics order 2 is suitable, continuing Verifying /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/dwi_C_connectom_st_b1200.bval is single shell ... b-shell bvalues [ 0. 1200.] Indices corresponding to b-shell 0.0 [ 0 8 15] Indices corresponding to b-shell 1200.0 [ 1 2 3 4 5 6 7 9 10 11 12 13 14] Verifying suitability of spherical harmonics order 2 for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/dwi_C_connectom_st_b1200.bval Determining maximum possible order of spherical harmonics for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/dwi_C_connectom_st_b1200.bval Maximum possible order is 2 for 13 non-zero gradients Spherical harmonics order 2 is suitable, continuing Verifying /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dwi_A_prisma_st_b1200.bval is single shell ... b-shell bvalues [ 0. 1200.] Indices corresponding to b-shell 0.0 [ 0 8 15] Indices corresponding to b-shell 1200.0 [ 1 2 3 4 5 6 7 9 10 11 12 13 14] Verifying suitability of spherical harmonics order 2 for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dwi_A_prisma_st_b1200.bval Determining maximum possible order of spherical harmonics for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dwi_A_prisma_st_b1200.bval Maximum possible order is 2 for 13 non-zero gradients Spherical harmonics order 2 is suitable, continuing Verifying /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/dwi_B_prisma_st_b1200.bval is single shell ... b-shell bvalues [ 0. 1200.] Indices corresponding to b-shell 0.0 [ 0 8 15] Indices corresponding to b-shell 1200.0 [ 1 2 3 4 5 6 7 9 10 11 12 13 14] Verifying suitability of spherical harmonics order 2 for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/dwi_B_prisma_st_b1200.bval Determining maximum possible order of spherical harmonics for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/dwi_B_prisma_st_b1200.bval Maximum possible order is 2 for 13 non-zero gradients Spherical harmonics order 2 is suitable, continuing Verifying /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/dwi_C_prisma_st_b1200.bval is single shell ... b-shell bvalues [ 0. 1200.] Indices corresponding to b-shell 0.0 [ 0 8 15] Indices corresponding to b-shell 1200.0 [ 1 2 3 4 5 6 7 9 10 11 12 13 14] Verifying suitability of spherical harmonics order 2 for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/dwi_C_prisma_st_b1200.bval Determining maximum possible order of spherical harmonics for /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/dwi_C_prisma_st_b1200.bval Maximum possible order is 2 for 13 non-zero gradients Spherical harmonics order 2 is suitable, continuing /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dti exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/harm exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/dti exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/harm exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/dti exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/harm exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dti exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/harm exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/dti exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/harm exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/dti exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py:63: UserWarning: /uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/harm exists, --force not specified, continuing with existing directory warnings.warn(f'{path} exists, --force not specified, continuing with existing directory') terminate called after throwing an instance of 'std::invalid_argument' what(): stoi /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh: line 931: 134992 Aborted ${ANTSPATH}/ImageMath selection/$TDIM vol0.nii.gz TimeSeriesSubset ${IMAGESETVARIABLE} ${range} /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh: line 916: cd: selection/: No such file or directory ls: cannot access *.nii.gz: No such file or directory -------------------------------------------------------------------------------------- Multivariate template construction using the following 2-tuples: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Creating template /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/template0.nii.gz from a population average image from the inputs. -------------------------------------------------------------------------------------- Usage: AverageImages ImageDimension Outputfname.nii.gz Normalize Compulsory arguments: ImageDimension: 2 or 3 (for 2 or 3 dimensional input). Outputfname.nii.gz: the name of the resulting image. Normalize: 0 - no normalization 1 - input images are divided by their mean before averaging; Laplacian sharpening is applied to the average 2 - input images are divided by their mean before averaging; no sharpening Images are resampled into the space of the largest input image. Example Usage: AverageImages 3 average.nii.gz 1 *.nii.gz Your initial template : /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/template0.nii.gz[0] was not created. This indicates trouble! You may want to check correctness of your input parameters. exiting. Traceback (most recent call last): File "/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py", line 538, in pipeline.run() File "/uufs/chpc.utah.edu/common/home/u0243256/.conda/envs/harmonization/lib/python3.9/site-packages/plumbum/cli/application.py", line 624, in run retcode = inst.main(*tailargs) File "/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py", line 513, in main self.createTemplate() File "/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/../../harmonization.py", line 227, in createTemplate antsMult(abspath(antsMultCaselist), self.templatePath) File "/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/buildTemplate.py", line 88, in antsMult check_call((' ').join([pjoin(SCRIPTDIR, 'antsMultivariateTemplateConstruction2_fixed_random_seed.sh'), File "/uufs/chpc.utah.edu/common/home/u0243256/.conda/envs/harmonization/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh -d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 64 -f 8x4x2x1 -o /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/ /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt' returned non-zero exit status 1. harmonization.py with --create --process --debug failed (harmonization) tests $ ```

tashrifbillah commented 2 years ago

This should be an ANTs issue, not ours:

/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh: line 931: 134992 Aborted ${ANTSPATH}/ImageMath selection/$TDIM vol0.nii.gz TimeSeriesSubset ${IMAGESETVARIABLE} ${range} /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh: line 916: cd: selection/: No such file or directory ls: cannot access *.nii.gz: No such file or directory

You can look up ANTs GitHub--the original script name is antsMultivariateTemplateConstruction2.sh.

njhunsak commented 2 years ago

I'm not sure it's an ANTs problem given that the input file listed doesn't exist:

(harmonization)  tests $ ls /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/
(harmonization)  tests $

There's no file named, antsMultCaselist.txt under the template directory. Therefore, when I run the command I get the error because it can't find any files, since there's no input information.

/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh \
-d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 64 -f 8x4x2x1 \
-o /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/ \
/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt

I think this is an issue with the harmonization.py script since this part of the script doesn't result in a file being created: https://github.com/pnlbwh/dMRIharmonization/blob/2a1001d8ef34b50ac647297267a8a34d47cebe1e/lib/harmonization.py#L213-L214

tashrifbillah commented 2 years ago

/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/

Does the executor have write permission inside above?
Check if connectom_prisma has unzipped properly:

/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/
Try touch antsMultCaselist.txt inside template/

suheyla2 commented 2 years ago

In addition to @tashrifbillah's suggestions: @njhunsak - Can you please check if the folders harm and dti empty? Can I access this path (/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/) using David's computer?

njhunsak commented 2 years ago

Yes I have full permission on all of these files as I am admin on our node.
Here's the tree of connectom_prisma:

tree

``` tree connectom_prisma connectom_prisma ├── connectom │ ├── A │ │ ├── dti │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_FA.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_GFA.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_L1.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_L2.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_L3.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_MD.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_MO.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_S0.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_V1.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_V2.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_V3.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_FA.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_GFA.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_L1.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_L2.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_L3.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_MD.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_MO.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_S0.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_V1.nii.gz │ │ │ ├── dwi_A_connectom_st_b1200_V2.nii.gz │ │ │ └── dwi_A_connectom_st_b1200_V3.nii.gz │ │ ├── dwi_A_connectom_st_b1200_bmapped.bval │ │ ├── dwi_A_connectom_st_b1200_bmapped.bvec │ │ ├── dwi_A_connectom_st_b1200_bmapped.nii.gz │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_bse.nii.gz │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled.bval │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled.bvec │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled.nii.gz │ │ ├── dwi_A_connectom_st_b1200_bse.nii.gz │ │ ├── dwi_A_connectom_st_b1200.bval │ │ ├── dwi_A_connectom_st_b1200.bvec │ │ ├── dwi_A_connectom_st_b1200_mask.nii.gz │ │ ├── dwi_A_connectom_st_b1200_mask_resampled.nii.gz │ │ ├── dwi_A_connectom_st_b1200.nii.gz │ │ └── harm │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_L0.nii.gz │ │ ├── dwi_A_connectom_st_b1200_bmapped_resampled_L2.nii.gz │ │ ├── dwi_A_connectom_st_b1200_L0.nii.gz │ │ └── dwi_A_connectom_st_b1200_L2.nii.gz │ ├── B │ │ ├── dti │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_FA.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_GFA.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_L1.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_L2.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_L3.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_MD.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_MO.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_S0.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_V1.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_V2.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_V3.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_FA.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_GFA.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_L1.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_L2.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_L3.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_MD.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_MO.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_S0.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_V1.nii.gz │ │ │ ├── dwi_B_connectom_st_b1200_V2.nii.gz │ │ │ └── dwi_B_connectom_st_b1200_V3.nii.gz │ │ ├── dwi_B_connectom_st_b1200_bmapped.bval │ │ ├── dwi_B_connectom_st_b1200_bmapped.bvec │ │ ├── dwi_B_connectom_st_b1200_bmapped.nii.gz │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_bse.nii.gz │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled.bval │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled.bvec │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled.nii.gz │ │ ├── dwi_B_connectom_st_b1200_bse.nii.gz │ │ ├── dwi_B_connectom_st_b1200.bval │ │ ├── dwi_B_connectom_st_b1200.bvec │ │ ├── dwi_B_connectom_st_b1200_mask.nii.gz │ │ ├── dwi_B_connectom_st_b1200_mask_resampled.nii.gz │ │ ├── dwi_B_connectom_st_b1200.nii.gz │ │ └── harm │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_L0.nii.gz │ │ ├── dwi_B_connectom_st_b1200_bmapped_resampled_L2.nii.gz │ │ ├── dwi_B_connectom_st_b1200_L0.nii.gz │ │ └── dwi_B_connectom_st_b1200_L2.nii.gz │ └── C │ ├── dti │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_FA.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_GFA.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_L1.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_L2.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_L3.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_MD.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_MO.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_S0.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_V1.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_V2.nii.gz │ │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_V3.nii.gz │ │ ├── dwi_C_connectom_st_b1200_FA.nii.gz │ │ ├── dwi_C_connectom_st_b1200_GFA.nii.gz │ │ ├── dwi_C_connectom_st_b1200_L1.nii.gz │ │ ├── dwi_C_connectom_st_b1200_L2.nii.gz │ │ ├── dwi_C_connectom_st_b1200_L3.nii.gz │ │ ├── dwi_C_connectom_st_b1200_MD.nii.gz │ │ ├── dwi_C_connectom_st_b1200_MO.nii.gz │ │ ├── dwi_C_connectom_st_b1200_S0.nii.gz │ │ ├── dwi_C_connectom_st_b1200_V1.nii.gz │ │ ├── dwi_C_connectom_st_b1200_V2.nii.gz │ │ └── dwi_C_connectom_st_b1200_V3.nii.gz │ ├── dwi_C_connectom_st_b1200_bmapped.bval │ ├── dwi_C_connectom_st_b1200_bmapped.bvec │ ├── dwi_C_connectom_st_b1200_bmapped.nii.gz │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_bse.nii.gz │ ├── dwi_C_connectom_st_b1200_bmapped_resampled.bval │ ├── dwi_C_connectom_st_b1200_bmapped_resampled.bvec │ ├── dwi_C_connectom_st_b1200_bmapped_resampled.nii.gz │ ├── dwi_C_connectom_st_b1200_bse.nii.gz │ ├── dwi_C_connectom_st_b1200.bval │ ├── dwi_C_connectom_st_b1200.bvec │ ├── dwi_C_connectom_st_b1200_mask.nii.gz │ ├── dwi_C_connectom_st_b1200_mask_resampled.nii.gz │ ├── dwi_C_connectom_st_b1200.nii.gz │ └── harm │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_L0.nii.gz │ ├── dwi_C_connectom_st_b1200_bmapped_resampled_L2.nii.gz │ ├── dwi_C_connectom_st_b1200_L0.nii.gz │ └── dwi_C_connectom_st_b1200_L2.nii.gz ├── connectom.txt ├── connectom.txt.modified ├── prisma │ ├── A │ │ ├── dti │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_FA.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_GFA.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_L1.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_L2.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_L3.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_MD.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_MO.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_S0.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_V1.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_V2.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_V3.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_FA.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_GFA.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_L1.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_L2.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_L3.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_MD.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_MO.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_S0.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_V1.nii.gz │ │ │ ├── dwi_A_prisma_st_b1200_V2.nii.gz │ │ │ └── dwi_A_prisma_st_b1200_V3.nii.gz │ │ ├── dwi_A_prisma_st_b1200_bmapped.bval │ │ ├── dwi_A_prisma_st_b1200_bmapped.bvec │ │ ├── dwi_A_prisma_st_b1200_bmapped.nii.gz │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_bse.nii.gz │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled.bval │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled.bvec │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled.nii.gz │ │ ├── dwi_A_prisma_st_b1200_bse.nii.gz │ │ ├── dwi_A_prisma_st_b1200.bval │ │ ├── dwi_A_prisma_st_b1200.bvec │ │ ├── dwi_A_prisma_st_b1200_mask.nii.gz │ │ ├── dwi_A_prisma_st_b1200_mask_resampled.nii.gz │ │ ├── dwi_A_prisma_st_b1200.nii.gz │ │ └── harm │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_L0.nii.gz │ │ ├── dwi_A_prisma_st_b1200_bmapped_resampled_L2.nii.gz │ │ ├── dwi_A_prisma_st_b1200_L0.nii.gz │ │ └── dwi_A_prisma_st_b1200_L2.nii.gz │ ├── B │ │ ├── dti │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_FA.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_GFA.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_L1.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_L2.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_L3.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_MD.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_MO.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_S0.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_V1.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_V2.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_V3.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_FA.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_GFA.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_L1.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_L2.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_L3.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_MD.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_MO.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_S0.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_V1.nii.gz │ │ │ ├── dwi_B_prisma_st_b1200_V2.nii.gz │ │ │ └── dwi_B_prisma_st_b1200_V3.nii.gz │ │ ├── dwi_B_prisma_st_b1200_bmapped.bval │ │ ├── dwi_B_prisma_st_b1200_bmapped.bvec │ │ ├── dwi_B_prisma_st_b1200_bmapped.nii.gz │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_bse.nii.gz │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled.bval │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled.bvec │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled.nii.gz │ │ ├── dwi_B_prisma_st_b1200_bse.nii.gz │ │ ├── dwi_B_prisma_st_b1200.bval │ │ ├── dwi_B_prisma_st_b1200.bvec │ │ ├── dwi_B_prisma_st_b1200_mask.nii.gz │ │ ├── dwi_B_prisma_st_b1200_mask_resampled.nii.gz │ │ ├── dwi_B_prisma_st_b1200.nii.gz │ │ └── harm │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_L0.nii.gz │ │ ├── dwi_B_prisma_st_b1200_bmapped_resampled_L2.nii.gz │ │ ├── dwi_B_prisma_st_b1200_L0.nii.gz │ │ └── dwi_B_prisma_st_b1200_L2.nii.gz │ └── C │ ├── dti │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_FA.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_GFA.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_L1.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_L2.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_L3.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_MD.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_MO.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_S0.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_V1.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_V2.nii.gz │ │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_V3.nii.gz │ │ ├── dwi_C_prisma_st_b1200_FA.nii.gz │ │ ├── dwi_C_prisma_st_b1200_GFA.nii.gz │ │ ├── dwi_C_prisma_st_b1200_L1.nii.gz │ │ ├── dwi_C_prisma_st_b1200_L2.nii.gz │ │ ├── dwi_C_prisma_st_b1200_L3.nii.gz │ │ ├── dwi_C_prisma_st_b1200_MD.nii.gz │ │ ├── dwi_C_prisma_st_b1200_MO.nii.gz │ │ ├── dwi_C_prisma_st_b1200_S0.nii.gz │ │ ├── dwi_C_prisma_st_b1200_V1.nii.gz │ │ ├── dwi_C_prisma_st_b1200_V2.nii.gz │ │ └── dwi_C_prisma_st_b1200_V3.nii.gz │ ├── dwi_C_prisma_st_b1200_bmapped.bval │ ├── dwi_C_prisma_st_b1200_bmapped.bvec │ ├── dwi_C_prisma_st_b1200_bmapped.nii.gz │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_bse.nii.gz │ ├── dwi_C_prisma_st_b1200_bmapped_resampled.bval │ ├── dwi_C_prisma_st_b1200_bmapped_resampled.bvec │ ├── dwi_C_prisma_st_b1200_bmapped_resampled.nii.gz │ ├── dwi_C_prisma_st_b1200_bse.nii.gz │ ├── dwi_C_prisma_st_b1200.bval │ ├── dwi_C_prisma_st_b1200.bvec │ ├── dwi_C_prisma_st_b1200_mask.nii.gz │ ├── dwi_C_prisma_st_b1200_mask_resampled.nii.gz │ ├── dwi_C_prisma_st_b1200.nii.gz │ └── harm │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_L0.nii.gz │ ├── dwi_C_prisma_st_b1200_bmapped_resampled_L2.nii.gz │ ├── dwi_C_prisma_st_b1200_L0.nii.gz │ └── dwi_C_prisma_st_b1200_L2.nii.gz ├── prisma.txt ├── prisma.txt.modified └── template ```

When I run the command touch antsMultCaselist.txt inside the template/ directory and then re-run the command, ./pipeline_test.sh the file gets deleted.
@suheyla2 As you can see from the tree structure the folders harm and dti are not empty.
@suheyla2 You should be able to access that path on David's computer / login yes.

suheyla2 commented 2 years ago

@njhunsak - I checked the path but it does not exist for me. Let's make sure that we set up the harmonization to a common folder or I have permission to access the folder.

njhunsak commented 2 years ago

@suheyla2 please try that path again.

suheyla2 commented 2 years ago

Still, no success! I will send an email to Tracy.

njhunsak commented 2 years ago

Unless David's account isn't part of the wilde group? I have permissions open on the apps directory:

$ ls -la /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/
drwxrwxrwx 24 u0243256 wilde        4096 Mar 15 07:35 .
drwxrwxr-x  9 root     wilde         141 Feb 22 11:36 ..
[...]
drwxrwxrwx  6 u0243256 wilde         216 Mar  9 13:25 dMRIharmonization

tashrifbillah commented 2 years ago

Can you reattempt the clone and test in your $HOME?

njhunsak commented 2 years ago

Same error running from $HOME. I even reinstalled ANTs to make sure I have the latest version. From what I can tell, antsMultivariateTemplateConstruction2_fixed_random_seed.sh requires that the images being used for the template have to all be in the same folder and the script should be submitted from that directory. It says so in the usage information:

Usage:

antsMultivariateTemplateConstruction2_fixed_random_seed.sh -d ImageDimension -o OutputPrefix 
<other options> <images>

Compulsory arguments (minimal command line requires SGE/PBS cluster, otherwise use -c and
  -j options):

     -d:  ImageDimension: 2 or 3 (for 2 or 3 dimensional registration of single volume)
   ImageDimension: 4 (for template generation of time-series data)

<images>  List of images in the current directory, eg *_t1.nii.gz. Should be at the end
          of the command.  Optionally, one can specify a .csv or .txt file where each
          line is the location of the input image.  One can also specify more than
          one file for each image for multi-modal template construction (e.g. t1 and t2).
          For the multi-modal case, the templates will be consecutively numbered (e.g.
          template0.nii.gz, template1.nii.gz, ...).

NB: All images to be added to the template should be in the same directory, and this
    script should be invoked from that directory.

[...]

From your code, in it appears that the images are kept in their original directories and a text file with full path names is generated. This won't work with antsMultivariateTemplateConstruction2_fixed_random_seed.sh and that's why I get my original error that ANTs can't find any images to use to generate a template.

If I copy the these files to the template directory:

cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dti/dwi_A_connectom_st_b1200_bmapped_resampled_FA.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_A_connectom_st_b1200_bmapped_resampled_FA.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/harm/dwi_A_connectom_st_b1200_bmapped_resampled_L0.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_A_connectom_st_b1200_bmapped_resampled_L0.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/dti/dwi_B_connectom_st_b1200_bmapped_resampled_FA.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_B_connectom_st_b1200_bmapped_resampled_FA.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/harm/dwi_B_connectom_st_b1200_bmapped_resampled_L0.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_B_connectom_st_b1200_bmapped_resampled_L0.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/dti/dwi_C_connectom_st_b1200_bmapped_resampled_FA.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_C_connectom_st_b1200_bmapped_resampled_FA.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/harm/dwi_C_connectom_st_b1200_bmapped_resampled_L0.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_C_connectom_st_b1200_bmapped_resampled_L0.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dti/dwi_A_prisma_st_b1200_bmapped_resampled_FA.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_A_prisma_st_b1200_bmapped_resampled_FA.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/harm/dwi_A_prisma_st_b1200_bmapped_resampled_L0.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_A_prisma_st_b1200_bmapped_resampled_L0.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/dti/dwi_B_prisma_st_b1200_bmapped_resampled_FA.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_B_prisma_st_b1200_bmapped_resampled_FA.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/harm/dwi_B_prisma_st_b1200_bmapped_resampled_L0.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_B_prisma_st_b1200_bmapped_resampled_L0.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/dti/dwi_C_prisma_st_b1200_bmapped_resampled_FA.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_C_prisma_st_b1200_bmapped_resampled_FA.nii.gz
cp -v ~/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/harm/dwi_C_prisma_st_b1200_bmapped_resampled_L0.nii.gz ~/dMRIharmonization/lib/tests/connectom_prisma/template/dwi_C_prisma_st_b1200_bmapped_resampled_L0.nii.gz

And create the antsMultCaselist.txt in the template directory:

vi ~/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt

with the following added to the text file:

dwi_A_connectom_st_b1200_bmapped_resampled_FA.nii.gz,dwi_A_connectom_st_b1200_bmapped_resampled_L0.nii.gz
dwi_B_connectom_st_b1200_bmapped_resampled_FA.nii.gz,dwi_B_connectom_st_b1200_bmapped_resampled_L0.nii.gz
dwi_C_connectom_st_b1200_bmapped_resampled_FA.nii.gz,dwi_C_connectom_st_b1200_bmapped_resampled_L0.nii.gz
dwi_A_prisma_st_b1200_bmapped_resampled_FA.nii.gz,dwi_A_prisma_st_b1200_bmapped_resampled_L0.nii.gz
dwi_B_prisma_st_b1200_bmapped_resampled_FA.nii.gz,dwi_B_prisma_st_b1200_bmapped_resampled_L0.nii.gz
dwi_C_prisma_st_b1200_bmapped_resampled_FA.nii.gz,dwi_C_prisma_st_b1200_bmapped_resampled_L0.nii.gz

Then, this command runs just fine:

cd ~/dMRIharmonization/lib/tests/connectom_prisma/template/
~/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh \
-d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 104 -f 8x4x2x1 \
antsMultCaselist.txt

I'm going to guess that dMRIharmonization is installed correctly since all the other checks worked just fine.

tashrifbillah commented 2 years ago

This won't work with antsMultivariateTemplateConstruction2_fixed_random_seed.sh and that's why I get my original error

./pipeline_test.sh is a long-standing and trusted test that has proven to be robust across many environments.

I even reinstalled ANTs to make sure I have the latest version.

I wonder if that is the culprit. I know a few things have changed in ANTs and we have tested using v2.3.0 only.

njhunsak commented 2 years ago

I installed ANTs v2.2.0 and the same issue persists (see log: pipelinetest.log).

I ran the other check listed, python -m unittest discover -v lib/tests/, and that works fine (see log: unittest.log.

If I create the antsMultCaselist.txt myself and put the absolute path of the files:

/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dti/dwi_A_connectom_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/harm/dwi_A_connectom_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/dti/dwi_B_connectom_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/harm/dwi_B_connectom_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/dti/dwi_C_connectom_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/harm/dwi_C_connectom_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dti/dwi_A_prisma_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/harm/dwi_A_prisma_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/dti/dwi_B_prisma_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/harm/dwi_B_prisma_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/dti/dwi_C_prisma_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/harm/dwi_C_prisma_st_b1200_bmapped_resampled_L0.nii.gz

And run this command from the template directory, I get the same error:

cd /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/
/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh \
-d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 64 -f 8x4x2x1 \
-o /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/  \
/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt

However, if I run this command from the template directory, it runs just fine:

cd /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/
/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh \
-d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 64 -f 8x4x2x1 \
-o /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/ \
antsMultCaselist.txt

Notice that in order for antsMultivariateTemplateConstruction2_fixed_random_seed.sh to run correctly, I have to use only the antsMultCaselist.txt and not the absolute path? There's a reason for that and is based on why ANTs says to invoke commands from the template directory:

https://github.com/ANTsX/ANTs/blob/1c5ae7c42f1149d26505819a710b50e6867d2f31/Scripts/antsMultivariateTemplateConstruction2.sh#L89-L90

I've used antsMultivariateTemplateConstruction2.sh previously outside of your pipeline and I know the program is very particular about the location of files, from what directory the command is submitted, and use of absolute paths. I've now shown two ways to get antsMultivariateTemplateConstruction2_fixed_random_seed.sh to run correctly.

Copy files to the template directory and list files without the absolute path in antsMultCaselist.txt and submit code from the template directory.
List files with absolute path in antsMultCaselist.txt and submit the code from the template directory.

In order to invoke the antsMultivariateTemplateConstruction2_fixed_random_seed.sh command, you have to be in the template directory that contains the antsMultCaselist.txt file. It doesn't run if you use the absolute path to antsMultCaselist.txt even if you are in the template directory. I'll show you why :

https://github.com/ANTsX/ANTs/blob/1c5ae7c42f1149d26505819a710b50e6867d2f31/Scripts/antsMultivariateTemplateConstruction2.sh#L900-L901

If you set IMAGESETVARIABLE to equal the absolute path on my system, /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt, then when the program tries to extract the extension with echo ${IMAGESETVARIABLE#*.}, the value will always be wrong. In my case the extension variable is set to utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt and that doesn't equal txt or csv. That's why I can't run the code from the harmonzation.py script.

So instead, if IMAGESETVARIABLE equals just antsMultCaselist.txt, which excludes the absolute path, the extension variable is now set to txt as it suppose to be set and everything runs just fine.

Any period anywhere in the absolute path is going to lead to issues based on the ANTs script. Could you update these lines in the harmonization.py and anywhere else in your code to be more compatible with the ANTs code and more universal for other systems?

https://github.com/pnlbwh/dMRIharmonization/blob/2a1001d8ef34b50ac647297267a8a34d47cebe1e/lib/harmonization.py#L226-L227

tashrifbillah commented 2 years ago

What does uname -a say?

njhunsak commented 2 years ago

 ~ $ uname -a
Linux notchpeak2 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

suheyla2 commented 2 years ago

@njhunsak - Thanks for reporting this. I wonder if there is another location where you can set up the pipeline that does not include dots in the absolute path? We have not observed this issue in the past since this type of path (chpc.utah.edu) is not common. We can note this, though. However, since the deadline is approaching and I do not have access to your data, this might be a better option.

njhunsak commented 2 years ago

@suheyla2 Having dots in pathnames is actually common. I've worked with nearly a dozen HPC systems and many have their base URL like this in their pathname. If they happen to not use their URL in the pathname, then I've had systems set usernames as the last name dot first name (hunsaker.naomi). Unfortunately, I can't control how the university sets its login and system name. This is an issue that will need to be addressed in the code instead.

tashrifbillah commented 2 years ago

Do:

cd dMRIharmonization
git pull origin dotted-path
cd lib/tests/
./pipeline_test.sh

and let us know your finding.

njhunsak commented 2 years ago

The pipeline_test.sh is still using the absolute path to the antsMultCaselist.txt file, which results in a error when trying to run antsMultivariateTemplateConstruction2_fixed_random_seed.sh:

subprocess.CalledProcessError: Command '/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh -d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 104 -f 8x4x2x1 -o /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/ /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt' returned non-zero exit status 1.

harmonization.py with --create --process --debug failed

I did confirm the new code in the buildTemplate.py script:

def antsMult(caselist, outPrefix):

    N_core=getenv('TEMPLATE_CONSTRUCT_CORES')

    # launch antsMultivariateTemplateConstruction2.sh from within template directory
    # https://github.com/pnlbwh/dMRIharmonization/issues/80
    with local.cwd(dirname(caselist)):
        check_call((' ').join([pjoin(SCRIPTDIR, 'antsMultivariateTemplateConstruction2_fixed_random_seed.sh'),
                               '-d', '3',
                               '-g', '0.2',
                               '-k', '2',
                               '-t', "BSplineSyN[0.1,26,0]",
                               '-r', '1',
                               '-c', '2',
                               '-j', str(N_core) if N_core else str(N_proc),
                               '-f', '8x4x2x1',
                               '-o', outPrefix,
                               caselist]), shell= True)

The only way antsMultivariateTemplateConstruction2_fixed_random_seed.sh will run correctly is if the command is submitted from within the template directory AND the text file that contains the list of images is submitted with NO path (e.g., antsMultCaselist.txt). The command needs to look like this when submitted:

/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh \
-d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 104 -f 8x4x2x1 \
-o /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/ \
antsMultCaselist.txt

tashrifbillah commented 2 years ago

The pipeline_test.sh is still using the absolute path to the antsMultCaselist.txt file, which results in a error

The above comment is contradictory to what was asked before:

List files with absolute path in antsMultCaselist.txt and submit the code from the template directory.

We followed that ask and provided a fix.

tashrifbillah commented 2 years ago

the text file that contains the list of images is submitted with NO path (e.g., antsMultCaselist.txt)

Clarify list of images and NO path. The two phrases are contradictory.

njhunsak commented 2 years ago

The antsMultCaselist.txt can contain the absolute path to the list of images. The command that submits antsMultCaselist.txt should not contain any path information. As I've explained above:

Create antsMultCaselist.txt in the template directory:

vi ~/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt

Copy and paste the list of images with absolute path information:

/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/dti/dwi_A_connectom_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/A/harm/dwi_A_connectom_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/dti/dwi_B_connectom_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/B/harm/dwi_B_connectom_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/dti/dwi_C_connectom_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/connectom/C/harm/dwi_C_connectom_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dti/dwi_A_prisma_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/harm/dwi_A_prisma_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/dti/dwi_B_prisma_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/B/harm/dwi_B_prisma_st_b1200_bmapped_resampled_L0.nii.gz
/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/dti/dwi_C_prisma_st_b1200_bmapped_resampled_FA.nii.gz,/uufs/chpc.utah.edu/common/home/u0243256/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/prisma/C/harm/dwi_C_prisma_st_b1200_bmapped_resampled_L0.nii.gz

Change into the template directory to submit antsMultivariateTemplateConstruction2_fixed_random_seed.sh:

cd /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/

Submit the following command with absolute path to antsMultCaselist.txt:

/uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/antsMultivariateTemplateConstruction2_fixed_random_seed.sh \
-d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 104 -f 8x4x2x1 \
-o /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/ \
antsMultCaselist.txt

tashrifbillah commented 2 years ago

The command that submits antsMultCaselist.txt should not contain any path information.

Where does it now?

njhunsak commented 2 years ago

I explained previously that the absolute path to antsMultCaselist.txt cannot be used when submitting antsMultivariateTemplateConstruction2_fixed_random_seed.sh:

If you set IMAGESETVARIABLE to equal the absolute path on my system, /uufs/chpc.utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt, then when the program tries to extract the extension with echo ${IMAGESETVARIABLE#*.}, the value will always be wrong. In my case the extension variable is set to utah.edu/common/home/tbicc-group1/apps/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt and that doesn't equal txt or csv. That's why I can't run the code from the harmonzation.py script.

So instead, if IMAGESETVARIABLE equals just antsMultCaselist.txt, which excludes the absolute path, the extension variable is now set to txt as it suppose to be set and everything runs just fine.

njhunsak commented 2 years ago

tashrifbillah commented 2 years ago

The last screenshot helps.

suheyla2 commented 2 years ago

Interestingly, it does work for me!

tashrifbillah commented 2 years ago

Suheyla is right. Regardless, please retry https://github.com/pnlbwh/dMRIharmonization/issues/80#issuecomment-1081434801

njhunsak commented 2 years ago

`basename()` was the change needed

Thank you for making this change based on my feedback since it fixes the issue of antsMultivariateTemplateConstruction2_fixed_random_seed.sh not wanting to run.

https://github.com/pnlbwh/dMRIharmonization/blob/f1f69293e4fdb4f435d6c42b7e975f77c4448958/lib/buildTemplate.py#L103

By using only the file name and not including the full path, ANTs can identify the file correctly.

Parallelization Options

Once I got the code running on my system, it took ~13 hours to run the pipeline_test.sh because parallelization was hardcoded in the antsMultivariateTemplateConstruction2_fixed_random_seed.sh command.

https://github.com/pnlbwh/dMRIharmonization/blob/f1f69293e4fdb4f435d6c42b7e975f77c4448958/lib/buildTemplate.py#L99

As a suggestion, it would be helpful to have the same options that ANTs provides when submitting the harmonzation.py command, so the end-user doesn't have to hunt through the code and manually change the parameters:

-c:  Control for parallel computation (default 0):
          0 = run serially
          1 = SGE qsub
          2 = use PEXEC (localhost)
          3 = Apple XGrid
          4 = PBS qsub
          5 = SLURM

The University of Utah CHPC system uses SLURM (v20.11.5) for job scheduling. When I changed '-c', '2', to '-c', '5', the process then only took 2 hours.

Results

With the code running correctly now, here are the results from our system:

04/02/22 03:05,mean meanFA,std meanFA
CONNECTOM,0.6888020758415321,0.010355104431533755
PRISMA_before,0.819265744652604,0.006880781750666151
PRISMA_after,0.6887081881685634,0.010201016058496677

The values aren't exactly the same as the table shown on Github. Is that OK?

02/24/20 11:37,mean meanFA,std meanFA
CONNECTOM,0.6799002461759734,0.007886013534889139
PRISMA_before,0.8016994786111754,0.010304926419301603
PRISMA_after,0.6763777736686049,0.010977445592601354

And here's the template/meanFAstat_ebarplot.png image:

meanFAstat_ebarplot

tashrifbillah commented 2 years ago

Thank you for confirming. I apologize for not clearly informing you about my basename() change last time.

because parallelization was hardcoded in the

We only work on localhost and so our program is set for -c 2 and -j all_available. Again, we do not have SLURM (-c 5). I shall have to think how to allow a variable -c from the command line. But it seems that you got it optimized for your system already. Regardless, you might benefit from reading https://github.com/pnlbwh/dMRIharmonization#multi-threading .

pnlbwh / dMRIharmonization