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pnlbwh / dMRIharmonization

Multi-site dMRI harmonization
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pipeline_test.sh #26

Closed fedemoro closed 5 years ago

fedemoro commented 5 years ago

I'm trying to test the pipeline (pipeline_test.sh) but I get the error below. The environment is set with these executables: antsMultivariateTemplateConstruction2.sh; antsApplyTransforms; antsRegistrationSyNQuick.sh; unring.a64

Computing shm_coeff of  prisma/C/dwi_C_prisma_st_b1200_resampled.nii.gz
/bin/sh: /rds/general/user/fmoro/home/unring_new/fsl/dMRIharmonization/lib/antsMultivariateTemplateConstruction2.sh: No such file or directory
Traceback (most recent call last):
  File "../../harmonization.py", line 405, in <module>
    pipeline.run()
  File "/rds/general/user/fmoro/home/miniconda3/envs/harmonization/lib/python3.7/site-packages/plumbum/cli/application.py", line 572, in run
    retcode = inst.main(*tailargs)
  File "../../harmonization.py", line 395, in main
    self.createTemplate()
  File "../../harmonization.py", line 214, in createTemplate
    antsMult(os.path.abspath(antsMultCaselist), self.templatePath)
  File "/rds/general/user/fmoro/home/unring_new/fsl/dMRIharmonization/lib/buildTemplate.py", line 97, in antsMult
    caselist]), shell= True)
  File "/rds/general/user/fmoro/home/miniconda3/envs/harmonization/lib/python3.7/subprocess.py", line 347, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/rds/general/user/fmoro/home/unring_new/fsl/dMRIharmonization/lib/antsMultivariateTemplateConstruction2.sh -d 3 -g 0.2 -k 2 -t BSplineSyN[0.1,26,0] -r 1 -c 2 -j 32 -f 8x4x2x1 -o ./template/ /rds/general/user/fmoro/home/unring_new/fsl/dMRIharmonization/lib/tests/connectom_prisma/template/antsMultCaselist.txt' returned non-zero exit status 127.
tashrifbillah commented 5 years ago

Which branch are you working on? The error is up there:

/bin/sh: /rds/general/user/fmoro/home/unring_new/fsl/dMRIharmonization/lib/antsMultivariateTemplateConstruction2.sh: No such file or directory

tashrifbillah commented 5 years ago

dipy-dti branch won't look for dMRIharmonization/lib/antsMultivariateTemplateConstruction2.sh. Rather, it will use ANTs provided antsMultivariateTemplateConstruction2.sh. The difference is, we specified random seed for reproduciblity of template in the former. Again, the former appears in branches spm-bspline or later.

My understanding is, your local branches are out of sync. Try git pull origin so your local branches are synced with our development.

tashrifbillah commented 5 years ago

If there is more problem, feel free to reopen the issue.

Meanwhile, design has been changed and made better in: https://github.com/pnlbwh/dMRIharmonization/releases/tag/v1.2.0