Prestats module crashes

[BlackHoleExelion]

Hello,

XCP prestats module crashes then breaks the whole xcp pipeline. The reason seems to be absence of xcp-struct, however, exactly same input files (dsn, cohort, fmriprep output, etc) worked fine on hosts without FIPS.

Environment: Singularity on PMACS HPC (FIPS enabled)

Version: XCP v1.2.3

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                  CURRENTLY PROCESSING MODULE:
                         ★ prestats ★
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[Delegating control to module]

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#  ⊗                 FMRI PREPROCESSING MODULE                 ⊗  #
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[I][/mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG.nii.gz]
[O][/mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/prestats]

Current processing step:
Ensure matching orientation
····································································
· Input: /mnt/project/oathes_group/xcp/temp_xcp/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG-prestats-048606424~TEMP~.nii.gz
· Template: /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
· Output root:
· checking the orientation of img and template
NATIVE:LPI TEMPLATE:RPI
· img and template orientation are not the same
· make it: LPI -> RPI

Current processing step:
getting data from fmriprep directory
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find: ‘/mnt/project/oathes_group/fmriprep/output/fmriprep/sub-C127/ses-TMSfMRI/..//anat/’: No such file or directory
find: ‘/mnt/project/oathes_group/fmriprep/output/fmriprep/sub-C127/ses-TMSfMRI/..//anat/’: No such file or directory

                   The template is MNI
                   xcpEngine only support MNI, PNC and OASIS templates for now

find: ‘/mnt/project/oathes_group/fmriprep/output/fmriprep/sub-C127/ses-TMSfMRI/..//anat/’: No such file or directory
find: ‘/mnt/project/oathes_group/fmriprep/output/fmriprep/sub-C127/ses-TMSfMRI/..//anat/’: No such file or directory
find: ‘/mnt/project/oathes_group/fmriprep/output/fmriprep/sub-C127/ses-TMSfMRI/..//anat/’: No such file or directory
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /tmp/ants/build/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1412:
itk::ERROR: ResampleImageFilter(0x557cb3293160): Input Primary is required but not set.
/xcpEngine/core/functions/exec_ants: line 1: 42211 Aborted                 ${ANTSPATH}/"${@}"
Image Exception : #22 :: ERROR: Could not open image /mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/prestats/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG_structmask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/xcpEngine/core/functions/exec_fsl: line 1: 42230 Aborted                 ${FSLDIR}/bin/"${@}"
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /tmp/ants/build/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1412:
itk::ERROR: ResampleImageFilter(0x559a9da1a210): Input Primary is required but not set.
/xcpEngine/core/functions/exec_ants: line 1: 42234 Aborted                 ${ANTSPATH}/"${@}"
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /tmp/ants/build/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1412:
itk::ERROR: ResampleImageFilter(0x562a5849a160): Input Primary is required but not set.
/xcpEngine/core/functions/exec_ants: line 1: 42253 Aborted                 ${ANTSPATH}/"${@}"
Cannot open volume /mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/prestats/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG_mask for reading!
Cannot open volume /mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/prestats/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG_mask for reading!
· generate new /mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG_spaces.json with spaceMetadata
source space map '/mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/prestats/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG_struct.nii.gz' is not an image
· Quality assessment
Error in readNifti(mask1path) :
  Failed to read image from path /mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/prestats/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG_segmentation.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(mask1path) :
  nifti_image_read: failed to find header file for '/mnt/project/oathes_group/xcp/output/sub-C127/ses-TMSfMRI/task-SP120/acq-PostIFG/prestats/sub-C127_ses-TMSfMRI_task-SP120_acq-PostIFG_segmentation.nii.gz'
Execution halted

[a3sha2]

can you post your design file?

[BlackHoleExelion]

Sorry, my bad. There was something wrong with the dir of fmriprep output, now it is working. Thanks for the reply!