Requested assistance in running xcp_d given below error:
Encountered index out of range error when using fmriprep data with --cifti-output flag. Had no issue running equivalent xcp_d command on NIfTI. Solutions to similar issues have been thus far unsuccessful. Appreciate the assistance.
Error:
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/run.py", line 1049, in build_workflow
retval["workflow"] = init_xcpd_wf(
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 202, in init_xcpd_wf
single_subj_wf = init_subject_wf(
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 502, in init_subject_wf
source_file=preproc_files[0],
IndexError: list index out of range
xcp_d command:
docker run --rm -it -v d:\\cognitive-networks\\data\\derivatives\\fmriprep_testing:/fmriprep:ro -v d:\\cognitive-networks\\data\\derivatives\\xcp_d_testing:/out:rw -v d:\\cognitive-networks\\data\\derivatives\\fmriprep_testing\\sourcedata\\freesurfer:/freesurfer:ro pennlinc/xcp_d:latest /fmriprep /out participant --participant-label MSC01 MSC02 --atlases Gordon --cifti --despike
fmriprep command:
fmriprep-docker D:\\cognitive-networks\\data D:\\cognitive-networks\\data\\derivatives\\fmriprep_testing participant --participant-label MSC01 MSC02 --task-id rest --low-mem --output-spaces MNI152NLin6Asym MNI152NLin2009cAsym --slice-time-ref 0 --cifti-output --fs-license-file D:\\cognitive-networks\\license.txt
Sample Functional Files:
05/08/2024 12:19 AM <DIR> .
05/06/2024 07:55 PM <DIR> ..
05/08/2024 12:19 AM 222,587 sub-MSC01_ses-func01_task-rest_desc-confounds_timeseries.json
05/08/2024 12:19 AM 3,456,558 sub-MSC01_ses-func01_task-rest_desc-confounds_timeseries.tsv
05/06/2024 08:04 PM 186 sub-MSC01_ses-func01_task-rest_desc-coreg_boldref.json
05/06/2024 08:04 PM 385,078 sub-MSC01_ses-func01_task-rest_desc-coreg_boldref.nii.gz
05/06/2024 07:55 PM 106 sub-MSC01_ses-func01_task-rest_desc-hmc_boldref.json
05/06/2024 07:55 PM 343,102 sub-MSC01_ses-func01_task-rest_desc-hmc_boldref.nii.gz
05/07/2024 08:46 PM 119 sub-MSC01_ses-func01_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
05/07/2024 08:46 PM 227 sub-MSC01_ses-func01_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
05/06/2024 07:58 PM 106 sub-MSC01_ses-func01_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
05/06/2024 07:58 PM 173,871 sub-MSC01_ses-func01_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
05/07/2024 09:05 PM 301,219 sub-MSC01_ses-func01_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
05/07/2024 09:05 PM 2,055 sub-MSC01_ses-func01_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
05/07/2024 09:11 PM 127 sub-MSC01_ses-func01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
05/07/2024 09:11 PM 240,005,908 sub-MSC01_ses-func01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
05/07/2024 09:05 PM 272,640 sub-MSC01_ses-func01_task-rest_space-MNI152NLin6Asym_boldref.nii.gz
05/07/2024 09:05 PM 1,913 sub-MSC01_ses-func01_task-rest_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
05/07/2024 09:11 PM 127 sub-MSC01_ses-func01_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.json
05/07/2024 09:11 PM 217,616,442 sub-MSC01_ses-func01_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
Sample Anatomy Files:
05/07/2024 07:55 PM 371 sub-MSC01_desc-brain_mask.json
05/07/2024 07:55 PM 86,969 sub-MSC01_desc-brain_mask.nii.gz
05/07/2024 12:28 AM 28 sub-MSC01_desc-preproc_T1w.json
05/07/2024 12:28 AM 51,798,944 sub-MSC01_desc-preproc_T1w.nii.gz
05/07/2024 07:57 PM 28 sub-MSC01_desc-preproc_T2w.json
05/07/2024 07:57 PM 53,159,415 sub-MSC01_desc-preproc_T2w.nii.gz
05/07/2024 07:58 PM 369 sub-MSC01_desc-ribbon_mask.json
05/07/2024 07:58 PM 251,818 sub-MSC01_desc-ribbon_mask.nii.gz
05/07/2024 08:02 PM 432,569 sub-MSC01_dseg.nii.gz
05/06/2024 08:31 PM 226 sub-MSC01_from-fsnative_to-T1w_mode-image_xfm.txt
05/07/2024 08:28 PM 89,918,425 sub-MSC01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
05/07/2024 08:28 PM 74,386,411 sub-MSC01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
05/06/2024 08:31 PM 229 sub-MSC01_from-T1w_to-fsnative_mode-image_xfm.txt
05/07/2024 08:28 PM 89,907,544 sub-MSC01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
05/07/2024 08:28 PM 74,381,069 sub-MSC01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
05/07/2024 07:56 PM 7,852,779 sub-MSC01_hemi-L_desc-reg_sphere.surf.gii
05/07/2024 07:55 PM 7,880,959 sub-MSC01_hemi-L_midthickness.surf.gii
05/07/2024 07:55 PM 7,887,127 sub-MSC01_hemi-L_pial.surf.gii
05/07/2024 08:32 PM 7,862,430 sub-MSC01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
05/07/2024 07:56 PM 7,867,292 sub-MSC01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
05/07/2024 07:56 PM 7,856,155 sub-MSC01_hemi-L_sphere.surf.gii
05/07/2024 07:55 PM 1,136,950 sub-MSC01_hemi-L_sulc.shape.gii
05/07/2024 07:55 PM 1,021,629 sub-MSC01_hemi-L_thickness.shape.gii
05/07/2024 07:55 PM 7,869,254 sub-MSC01_hemi-L_white.surf.gii
05/07/2024 07:56 PM 7,837,645 sub-MSC01_hemi-R_desc-reg_sphere.surf.gii
05/07/2024 07:55 PM 7,813,843 sub-MSC01_hemi-R_midthickness.surf.gii
05/07/2024 07:55 PM 7,823,447 sub-MSC01_hemi-R_pial.surf.gii
05/07/2024 08:32 PM 7,839,643 sub-MSC01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
05/07/2024 07:56 PM 7,842,142 sub-MSC01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
05/07/2024 07:56 PM 7,841,585 sub-MSC01_hemi-R_sphere.surf.gii
05/07/2024 07:55 PM 1,136,006 sub-MSC01_hemi-R_sulc.shape.gii
05/07/2024 07:55 PM 1,019,017 sub-MSC01_hemi-R_thickness.shape.gii
05/07/2024 07:55 PM 7,799,482 sub-MSC01_hemi-R_white.surf.gii
05/07/2024 08:02 PM 1,297,682 sub-MSC01_label-CSF_probseg.nii.gz
05/07/2024 08:02 PM 2,310,954 sub-MSC01_label-GM_probseg.nii.gz
05/07/2024 08:02 PM 1,207,825 sub-MSC01_label-WM_probseg.nii.gz
05/07/2024 08:33 PM 578,800 sub-MSC01_space-fsLR_den-91k_curv.dscalar.nii
05/07/2024 08:33 PM 425 sub-MSC01_space-fsLR_den-91k_curv.json
05/07/2024 08:33 PM 578,800 sub-MSC01_space-fsLR_den-91k_sulc.dscalar.nii
05/07/2024 08:33 PM 425 sub-MSC01_space-fsLR_den-91k_sulc.json
05/07/2024 08:33 PM 578,800 sub-MSC01_space-fsLR_den-91k_thickness.dscalar.nii
05/07/2024 08:33 PM 425 sub-MSC01_space-fsLR_den-91k_thickness.json
05/07/2024 08:30 PM 21 sub-MSC01_space-MNI152NLin2009cAsym_desc-brain_mask.json
05/07/2024 08:30 PM 92,765 sub-MSC01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
05/07/2024 08:29 PM 27 sub-MSC01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
05/07/2024 08:29 PM 15,134,419 sub-MSC01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
05/07/2024 08:30 PM 432,854 sub-MSC01_space-MNI152NLin2009cAsym_dseg.nii.gz
05/07/2024 08:29 PM 7,505,051 sub-MSC01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
05/07/2024 08:29 PM 11,598,206 sub-MSC01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
05/07/2024 08:29 PM 7,507,305 sub-MSC01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
05/07/2024 08:30 PM 21 sub-MSC01_space-MNI152NLin6Asym_desc-brain_mask.json
05/07/2024 08:30 PM 89,464 sub-MSC01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
05/07/2024 08:29 PM 27 sub-MSC01_space-MNI152NLin6Asym_desc-preproc_T1w.json
05/07/2024 08:29 PM 14,609,397 sub-MSC01_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
05/07/2024 08:30 PM 415,632 sub-MSC01_space-MNI152NLin6Asym_dseg.nii.gz
05/07/2024 08:28 PM 7,255,541 sub-MSC01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
05/07/2024 08:28 PM 11,220,197 sub-MSC01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
05/07/2024 08:28 PM 7,225,295 sub-MSC01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
58 File(s) 638,152,158 bytes