DCAN processing error

ssinha · January 29, 2025, 7:23pm

Summary of what happened:

Hello, I recently joined this forum after starting my work with XCP-D. In short, while I am able to run XCP-D in other formats, processing with DCAN input has been a major hurdle. When I include the “–input-type dcan” argument, I keep receiving a “FileNotFoundError” as shown below:

Apologies for my long query. I am happy to provide any additional information that may be needed.

Thank you,
Saptarshi

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run /data/nil-external/ccp/XCP-D/xcp_d_dec2024.simg \
/data/nil-external/ccp/XCP-D/ECDMT10000/derivatives \
/data/nil-external/ccp/XCP-D/xcp_dcan_output_jan-2025 \
participant \
--combine-runs \
--nthreads 1 \
--omp-nthreads 1 \
--mem-gb 10 \
--smoothing 2 \
--min-coverage 0.5 \
--min-time 100 \
--dummy-scans 6 \
--random-seed 0 \
--bpf-order 2 \
--despike \
--lower-bpf 0.01 \
--upper-bpf 0.08 \
-p 36P \
--motion-filter-type notch \
--band-stop-min 15 \
--band-stop-max 25 \
--motion-filter-order 4 \
--head-radius auto\
-f 0.3 \
--file-format cifti \
--warp-surfaces-native2std \
--input-type dcan \
--mode abcd \
--linc-qc y

Version:

XCP-D v0.10.1

Environment (Docker, Singularity / Apptainer, custom installation):

XCP-D was installed via the Singularity Container technology as an .simg file.

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

FileNotFoundError: No BOLD data found in allowed spaces (fsLR).
Query: {'datatype': 'func', 'desc': ['preproc', None], 'suffix': 'bold', 'extension': '.dtseries.nii', 'space': 'fsLR'}

In addition, some of the extraneous arguments were not recognized by XCP-D. I removed them from my command structure but the exact error messages are provided below. I should also note that I obtained these specific arguments from an associate and I could not find information regarding these from the documentation.

xcp_d: error: unrecognized arguments: --exact-time 300 480 600*
xcp_d: error: unrecognized arguments: --dcan-qc

Finally, while removing the --input-type dcan argument works and XCP-D runs to completion, I still receive the following error upon completion:

250127-19:35:24,687 nipype.workflow CRITICAL:
         XCP-D failed: 12 raised. Re-raising first.
2025-01-27 19:35:24,687 [CRITICAL] XCP-D failed: 12 raised. Re-raising first.
2025-01-27 19:35:42,865 [ WARNING] WARNING: The 'strip_cdata' option of HTMLParser() has never done anything and will eventually be removed.

Screenshots / relevant information:

Steven · January 29, 2025, 7:28pm

Hi @ssinha, and welcome to neurostars!

Did you run surface processing during preprocessing?

What kind of preprocessing did you run?

That is not an argument. Please update to most recent version (0.10.5) and check inputs here: Running XCP-D — xcp_d 0.10.5.dev18+g5c7821a documentation

ssinha:

**250127-19:35:24,687 nipype.workflow CRITICAL:**
**         XCP-D failed: 12 raised. Re-raising first.**
**2025-01-27 19:35:24,687 [CRITICAL] XCP-D failed: 12 raised. Re-raising first.**
**2025-01-27 19:35:42,865 [ WARNING] WARNING: The 'strip_cdata' option of HTMLParser() has never done anything and will eventually be removed.**

Can you provide the full traceback that also shows the error? But make sure you address the other suggestions first and see if you still get errors.

Best,
Steven

ssinha · January 29, 2025, 8:28pm

Hello Steven,

Many thanks for your quick response! I deeply appreciate the support. I should have added some more information in my original email, but will provide them now and also try to address your queries.

Regarding the input data that I am using, I did not pre-process it myself but it was conducted by my colleagues at the Cognitive Control & Psychopathology Laboratory in Washington University in St. Louis as part of the ECDMT project. I believe my colleagues used fMRIprep pipelines for preprocessing.

Regarding the extra arguments, thank you for letting me know about the invalidity of the “--exact-time 300 480 600” argument. Is it the same case with the “--dcan-qc” argument? The only options I could find were those involving “--linc-qc” and “--abcc-qc”, but not about “--dcan-qc” in the documentation. We obtained these extra arguments from our UPenn associates.

Regarding the FileNotFoundError, I referred to an earlier post in this forum regarding this issue and also the marked solution. It appears that the required files are present in the directory. Here are the observations I made:

sinhas@ccplinux1% ls *desc-preproc_T1w.nii.gz -l
-rw-r--r--+ 1 sinhas input 56098408 Dec 16 03:02 sub-ECDMT10000_ses-1_desc-preproc_T1w.nii.gz
-rw-r--r--+ 1 sinhas input 15258395 Dec 16 03:01 sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
-rw-r--r--+ 1 sinhas input   957005 Dec 16 03:02 sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
sinhas@ccplinux1% ls *desc-brain_mask.nii.gz -l
-rw-r--r--+ 1 sinhas input 86094 Dec 16 03:01 sub-ECDMT10000_ses-1_desc-brain_mask.nii.gz
-rw-r--r--+ 1 sinhas input 92203 Dec 16 03:02 sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
-rw-r--r--+ 1 sinhas input 10785 Dec 16 03:01 sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
sinhas@ccplinux1% ls *from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5 -l
-rw-r--r--+ 1 sinhas input 74500580 Dec 16 03:01 sub-ECDMT10000_ses-1_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
sinhas@ccplinux1% ls *from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5 -l
-rw-r--r--+ 1 sinhas input 74503278 Dec 16 03:02 sub-ECDMT10000_ses-1_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
sinhas@ccplinux1% pwd
/data/nil-external/ccp/XCP-D/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat

Regarding the the traceback error, here is a snippet for your reference:

250127-19:35:24,355 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
2025-01-27 19:35:24,355 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
250127-19:35:24,368 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
2025-01-27 19:35:24,368 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
250127-19:35:24,379 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,379 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250127-19:35:24,388 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-01-27 19:35:24,388 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250127-19:35:24,396 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,396 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250127-19:35:24,403 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-01-27 19:35:24,403 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250127-19:35:24,411 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
2025-01-27 19:35:24,411 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
250127-19:35:24,418 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,418 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
250127-19:35:24,426 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,426 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250127-19:35:24,433 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,433 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
250127-19:35:24,441 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,441 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250127-19:35:24,449 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,449 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,549 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,563 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,573 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,583 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,593 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,603 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,612 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,622 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,632 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,642 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,651 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,662 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
250127-19:35:24,687 nipype.workflow CRITICAL:
         XCP-D failed: 12 raised. Re-raising first.
2025-01-27 19:35:24,687 [CRITICAL] XCP-D failed: 12 raised. Re-raising first.
2025-01-27 19:35:42,865 [ WARNING] WARNING: The 'strip_cdata' option of HTMLParser() has never done anything and will eventually be removed.
sinhas@ccplinux1%

Thanks again for your support!

Saptarshi

Steven · January 29, 2025, 8:32pm

Hi @ssinha,

In that case you should use --input-type fmriprep (or leave blank since thats the default). Was surface preprocessing performed (CIFTI is the fslr filetype being requested)?

Yes, that argument has been deprecated. All current arguments are in the link I posted earlier.

That solution was for a different error [FileNotFoundError: No BOLD NIfTI or transforms found to allowed space (MNIInfant)].

Best,
Steven

ssinha · January 30, 2025, 8:37pm

Hello Steven,

Thank you for your assistance. I wanted to share that I consulted with my colleagues and can confirm that the input ECDMT data was pre-processed using fMRIprep. I can also confirm that surface preprocessing was performed.

I wanted to add some more clarifications regarding the errors. There are two errors I am trying to resolve right now, one that involves processing with DCAN-type input, and the other involves a more generic error.

Pasted below is the error message corresponding to DCAN-type input. Given the nature of this error, I referred to the other post and the marked solution, and was able to locate the necessary files that were listed. However, since the input data was pre-processed using fMRIprep, should the input data be instead pre-processed in a different format such that I can then use the “input-type dcan” argument?

FileNotFoundError: No BOLD data found in allowed spaces (fsLR).

Query: {‘datatype’: ‘func’, ‘desc’: [‘preproc’, None], ‘suffix’: ‘bold’, ‘extension’: ‘.dtseries.nii’, ‘space’: ‘fsLR’}

Found files:

The second error arises even without the “–input-type” argument. I posted the snippet of the traceback error in the preceding response. I am wondering if this is a more pervasive issue that I should resolve with any arguments that are possibly creating a conflict in my command.

Thanks,
Saptarshi

Steven · January 30, 2025, 8:49pm

Hi @ssinha,

If you preprocessed data with fmriprep, then use the --input-type fmriprep (or leave blank since that is default).

What you posted seems cut off before the found files which would help me debug. Can you provide the tree directory structure of a failing subject’s fmriprep outputs?

Best,
Steven

ssinha · January 30, 2025, 9:28pm

Hello Steven,

Pasted below is the directory structure of the source input file:

/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/.license
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/.license/freesurfer
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/logs
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/stats
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/touch
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/src
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/scripts
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/mri
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/mri/orig
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/mri/transforms
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/mri/transforms/bak
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/label
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/trash
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/surf
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/bem
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/xhemi/tmp
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/mri.2mm
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/surf
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/scripts
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/mri
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/mri/transforms
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/mri/transforms/bak
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/mri/orig
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage/label
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/trash
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/mri
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/mri/orig
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/mri/transforms
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/mri/transforms/bak
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/stats
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/scripts
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/label
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/surf
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/touch
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/sub-ECDMT10000/tmp
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5/tmp
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5/label
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5/stats
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5/surf
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5/scripts
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5/mri
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sourcedata/freesurfer/fsaverage5/mri/transforms
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/figures
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/log
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/log/20231218-134030_b1e275be-9ad4-435a-ba17-6e98a31dfc05
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat

Also, for your reference, here is the full message that I received that preceded the FileNotFoundError message:

2025-01-30 14:08:42,277 [ WARNING] WARNING: The sentry_sdk.metrics module is deprecated and will be removed in the next major release. Sentry will reject all metrics sent after October 7, 2024. Learn more: https://sentry.zendesk.com/hc/en-us/articles/26369339769883-Upcoming-API-Changes-to-Metrics
2025-01-30 14:08:42,327 [ WARNING] WARNING: `sentry_sdk.Hub` is deprecated and will be removed in a future major release. Please consult our 1.x to 2.x migration guide for details on how to migrate `Hub` usage to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x
2025-01-30 14:08:43,030 [ WARNING] A valid FreeSurfer license file is recommended. Set the FS_LICENSE environment variable or use the '--fs-license-file' flag.
250130-14:08:46,617 nipype.utils WARNING:
         convert_dcan2bids is an experimental function.
2025-01-30 14:08:46,617 [ WARNING] convert_dcan2bids is an experimental function.
250130-14:08:46,634 nipype.utils INFO:
         Processing sub-ECDMT10000
2025-01-30 14:08:46,634 [    INFO] Processing sub-ECDMT10000
250130-14:08:46,637 nipype.utils INFO:
         Converted dataset folder already exists. Skipping conversion.
2025-01-30 14:08:46,637 [    INFO] Converted dataset folder already exists. Skipping conversion.
2025-01-30 14:08:48,596 [ WARNING] WARNING: sentry_sdk.configure_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-configuring
2025-01-30 14:09:11,749 [ WARNING] WARNING: The sentry_sdk.metrics module is deprecated and will be removed in the next major release. Sentry will reject all metrics sent after October 7, 2024. Learn more: https://sentry.zendesk.com/hc/en-us/articles/26369339769883-Upcoming-API-Changes-to-Metrics
2025-01-30 14:09:11,783 [ WARNING] WARNING: `sentry_sdk.Hub` is deprecated and will be removed in a future major release. Please consult our 1.x to 2.x migration guide for details on how to migrate `Hub` usage to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x
250130-14:09:14,997 nipype.workflow IMPORTANT:
         Running XCP-D version 0.10.1
2025-01-30 14:09:14,997 [IMPORTANT] Running XCP-D version 0.10.1
250130-14:09:15,23 nipype.workflow IMPORTANT:
         Building XCP-D's workflow:
           * Preprocessing derivatives path: /data/nil-external/ccp/XCP-D/working_dir/dset_bids/derivatives/dcan.
           * Participant list: ['ECDMT10000'].
           * Run identifier: 20250130-140833_2741b6b5-c7af-4170-baf2-c94f6bf98cb3.
           * Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
2025-01-30 14:09:15,023 [IMPORTANT] Building XCP-D's workflow:
           * Preprocessing derivatives path: /data/nil-external/ccp/XCP-D/working_dir/dset_bids/derivatives/dcan.
           * Participant list: ['ECDMT10000'].
           * Run identifier: 20250130-140833_2741b6b5-c7af-4170-baf2-c94f6bf98cb3.
           * Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
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/workflow.py", line 100, in build_workflow
    retval['workflow'] = init_xcpd_wf()
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 81, in init_xcpd_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 127, in init_single_subject_wf
    subj_data = collect_data(
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/utils/bids.py", line 212, in collect_data
    raise FileNotFoundError(
FileNotFoundError: No BOLD data found in allowed spaces (fsLR).

Query: {'datatype': 'func', 'desc': ['preproc', None], 'suffix': 'bold', 'extension': '.dtseries.nii', 'space': 'fsLR'}

Found files:

Regarding the second error involving [CRITICAL] XCP-D failed: 12 raised. Re-raising first. (full traceback message posted earlier), I should also note that I get this error only after XCP-D runs to completion after like ~3h.

Thanks,
Saptarshi

Steven · January 30, 2025, 9:36pm

Hi @ssinha,

The tree does not go far enough, as I cannot see what is in the subject’s func folder.

Best,
Steven

ssinha · January 30, 2025, 9:44pm

No worries, here is the full content for all of the func, fmap, and anat folders:

/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-fsLR_den-91k_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_boldref.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_hemi-R_space-fsaverage5_bold.func.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_hemi-R_space-fsaverage5_bold.func.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_from-scanner_to-T1w_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-aparcaseg_dseg.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-aparcaseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-aseg_dseg.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_hemi-L_space-fsaverage5_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_from-T1w_to-scanner_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_desc-confounds_timeseries.tsv
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_boldref.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_boldref.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_hemi-L_space-fsaverage5_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-aseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-aparcaseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-fsLR_den-91k_bold.dtseries.nii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_boldref.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-fsLR_den-91k_bold.dtseries.nii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-aseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_from-scanner_to-boldref_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_desc-confounds_timeseries.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_from-scanner_to-T1w_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_desc-confounds_timeseries.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_from-scanner_to-boldref_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_boldref.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_desc-confounds_timeseries.tsv
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_hemi-L_space-fsaverage5_bold.func.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_hemi-L_space-fsaverage5_bold.func.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-aseg_dseg.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_hemi-R_space-fsaverage5_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-aparcaseg_dseg.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_from-T1w_to-scanner_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_hemi-R_space-fsaverage5_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_boldref.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEfnl_run-1_space-fsLR_den-91k_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/func/sub-ECDMT10000_ses-1_task-MOVIEdm_run-1_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00001_desc-preproc_fieldmap.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00000_desc-epi_fieldmap.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00001_desc-epi_fieldmap.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00001_desc-preproc_fieldmap.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00001_desc-coeff_fieldmap.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/fmap/sub-ECDMT10000_ses-1_fmapid-auto00000_desc-preproc_fieldmap.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_inflated.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_midthickness.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_pial.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-preproc_T1w.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-ribbon_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_midthickness.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_label-GM_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-fsLR_den-91k_thickness.dscalar.nii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_sulc.shape.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-fsLR_den-91k_sulc.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_thickness.shape.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_sulc.shape.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_label-WM_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_desc-reg_sphere.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-fsLR_den-91k_curv.dscalar.nii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_pial.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-brain_mask.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_label-GM_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-fsLR_den-91k_sulc.dscalar.nii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_thickness.shape.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-brain_mask.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-preproc_T2w.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_label-CSF_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_label-CSF_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-preproc_T2w.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_from-T1w_to-fsnative_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_curv.shape.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_curv.shape.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-aparcaseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-aseg_dseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-fsLR_den-91k_curv.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_inflated.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-brain_mask.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_from-fsnative_to-T1w_mode-image_xfm.txt
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-fsLR_den-91k_thickness.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_desc-reg_sphere.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_label-WM_probseg.nii.gz
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-R_white.surf.gii
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_dseg.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_desc-preproc_T1w.json
/data/nil-external/ccp/ECDMT/fMRIPrep_PREPROCESSED/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat/sub-ECDMT10000_ses-1_hemi-L_white.surf.gii

Steven · January 30, 2025, 9:52pm

Hi @ssinha,

Thanks, I see there are CIFTIs there (the fsLR dtseries.nii). I see in your singularity run command, you did not mount any drives. Perhaps XCP_D just isn’t finding data because you are not mounting your folders to the container. Can you mount relevant folders with the -B argument? Also as a rule of thumb you should add the -e flag to make sure you aren’t accidentally bringing in your environmental variables to the container.

Best,
Steven

ssinha · February 3, 2025, 9:52pm

Hello Steven,

Many thanks for your prior assistance!

I wanted to follow up on this to share that I am still receiving the [CRITICAL] XCP-D failed error. Here’s the full message:

250203-15:27:17,890 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
2025-02-03 15:27:17,890 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
250203-15:27:17,898 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
2025-02-03 15:27:17,898 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
250203-15:27:17,907 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,907 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250203-15:27:17,914 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-02-03 15:27:17,914 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250203-15:27:17,922 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,922 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250203-15:27:17,929 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-02-03 15:27:17,929 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250203-15:27:17,937 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
2025-02-03 15:27:17,937 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
250203-15:27:17,944 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:17,944 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
250203-15:27:17,951 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,951 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250203-15:27:17,959 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:17,959 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
250203-15:27:17,966 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,966 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250203-15:27:17,974 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:17,974 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:18,131 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,148 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,158 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,168 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,177 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,187 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,196 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,206 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,216 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,225 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,234 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,244 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
250203-15:27:18,268 nipype.workflow CRITICAL:
         XCP-D failed: 12 raised. Re-raising first.
2025-02-03 15:27:18,268 [CRITICAL] XCP-D failed: 12 raised. Re-raising first.
2025-02-03 15:27:29,998 [ WARNING] WARNING: The 'strip_cdata' option of HTMLParser() has never done anything and will eventually be removed.

I did include the -B argument this time but could not find information about the -e flag. Here is the full command structure:

singularity run \
-B /scratch1/sinha/ECDMT10000/derivatives \
/data/nil-external/ccp/XCP-D/xcp_d_dec2024.simg \
/scratch1/sinha/ECDMT10000/derivatives \
/data/nil-external/ccp/XCP-D/xcp_sample_output_feb03-2025 \
participant \
--combine-runs \
--nthreads 1 \
--omp-nthreads 1 \
--mem-gb 10 \
--smoothing 2 \
--min-coverage 0.5 \
--min-time 100 \
--dummy-scans 6 \
--random-seed 0 \
--bpf-order 2 \
--despike \
--lower-bpf 0.01 \
--upper-bpf 0.08 \
-p 36P \
--motion-filter-type notch \
--band-stop-min 15 \
--band-stop-max 25 \
--motion-filter-order 4 \
--head-radius auto\
-f 0.3 \
--file-format cifti \
--warp-surfaces-native2std \
--mode abcd \
--abcc-qc y

Is there any additional steps that I should try and maybe also rectify the command structure?

Thanks,
Saptarshi

Steven · February 3, 2025, 10:50pm

H @ssinha,

Well that looks like a different error at least. It looks like you moved some data to scratch space to run, which is fine but I do not know what you copied there or how you did it.

Is there anymore traceback you can share? That doesn’t seem to actually say what the error is.

It is one of the arguments that can go in the singularity run preamble.

It doesn’t look like this drive was mounted.

Best,
Steven

ssinha · February 3, 2025, 11:22pm

Hello Steven,

Thanks for your quick response!
Due to updated requirements in our research group, I am no longer including the --input-type -dcan argument and will temporarily focus on the default (fmriprep) input type. Hence, the previous FileNotFoundError is not a major issue right now. For the current error, I encountered this earlier and pasted it in one of my preceding responses (Jan 29, 2025 at 2:28 pm).

I also moved the data to a scratch space for running multiple tests to resolve the current error.

I will retry by mounting the output drive as well.

It looks like the traceback before the error message is more generic in nature. Here’s a sample below for your reference. I should also note that this arises after XCP-D runs to completion (after like ~3h).

250203-15:26:28,730 nipype.workflow INFO:
         [Node] Setting-up "_cifti_to_tsv14" in "/data/nil-external/ccp/XCP-D/working_dir/xcp_d_0_10_wf/sub_ECDMT10000_wf/postprocess_1_wf/connectivity_wf/parcellate_alff_wf/cifti_to_tsv/mapflow/_cifti_to_tsv14".
2025-02-03 15:26:28,730 [    INFO] [Node] Setting-up "_cifti_to_tsv14" in "/data/nil-external/ccp/XCP-D/working_dir/xcp_d_0_10_wf/sub_ECDMT10000_wf/postprocess_1_wf/connectivity_wf/parcellate_alff_wf/cifti_to_tsv/mapflow/_cifti_to_tsv14".
250203-15:26:28,733 nipype.workflow INFO:
         [Node] Cached "_cifti_to_tsv14" - collecting precomputed outputs
2025-02-03 15:26:28,733 [    INFO] [Node] Cached "_cifti_to_tsv14" - collecting precomputed outputs
250203-15:26:28,734 nipype.workflow INFO:
         [Node] "_cifti_to_tsv14" found cached.
2025-02-03 15:26:28,734 [    INFO] [Node] "_cifti_to_tsv14" found cached.
250203-15:26:28,735 nipype.workflow INFO:
         [Node] Setting-up "_cifti_to_tsv15" in "/data/nil-external/ccp/XCP-D/working_dir/xcp_d_0_10_wf/sub_ECDMT10000_wf/postprocess_1_wf/connectivity_wf/parcellate_alff_wf/cifti_to_tsv/mapflow/_cifti_to_tsv15".
2025-02-03 15:26:28,735 [    INFO] [Node] Setting-up "_cifti_to_tsv15" in "/data/nil-external/ccp/XCP-D/working_dir/xcp_d_0_10_wf/sub_ECDMT10000_wf/postprocess_1_wf/connectivity_wf/parcellate_alff_wf/cifti_to_tsv/mapflow/_cifti_to_tsv15".
250203-15:26:28,738 nipype.workflow INFO:
         [Node] Cached "_cifti_to_tsv15" - collecting precomputed outputs
2025-02-03 15:26:28,738 [    INFO] [Node] Cached "_cifti_to_tsv15" - collecting precomputed outputs
250203-15:26:28,738 nipype.workflow INFO:
         [Node] "_cifti_to_tsv15" found cached.
2025-02-03 15:26:28,738 [    INFO] [Node] "_cifti_to_tsv15" found cached.
250203-15:27:17,890 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
2025-02-03 15:27:17,890 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
250203-15:27:17,898 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
2025-02-03 15:27:17,898 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
250203-15:27:17,907 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,907 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250203-15:27:17,914 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-02-03 15:27:17,914 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250203-15:27:17,922 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,922 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250203-15:27:17,929 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-02-03 15:27:17,929 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250203-15:27:17,937 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
2025-02-03 15:27:17,937 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
250203-15:27:17,944 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:17,944 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
250203-15:27:17,951 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,951 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250203-15:27:17,959 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:17,959 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
250203-15:27:17,966 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-02-03 15:27:17,966 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250203-15:27:17,974 nipype.workflow ERROR:
         could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:17,974 [   ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-02-03 15:27:18,131 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,148 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,158 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,168 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,177 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,187 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,196 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,206 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,216 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,225 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,234 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-02-03 15:27:18,244 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
250203-15:27:18,268 nipype.workflow CRITICAL:
         XCP-D failed: 12 raised. Re-raising first.
2025-02-03 15:27:18,268 [CRITICAL] XCP-D failed: 12 raised. Re-raising first.
2025-02-03 15:27:29,998 [ WARNING] WARNING: The 'strip_cdata' option of HTMLParser() has never done anything and will eventually be removed.
sinhas@ccplinux1%

Pardon me for my ignorance with singularity containers. I was wondering if you could share a sample command with the -e flag or if there is a documentation that I can refer to regarding its usage.

Thanks,
Saptarshi

Steven · February 3, 2025, 11:26pm

Hi @ssinha,

You can just put -e before your -B.

I am not sure why this is temporary, as we established earlier that the outputs are from fMRIPrep.

That message still doesn’t appear to have the full traceback. Can you share more or even just attach a .txt file of everything?

It looks like this is just something with the executive summary, which has been getting overhauled recently, but importantly it sounds like your output files are being created?

Best,
Steven

ssinha · February 3, 2025, 11:50pm

Hello Steven,

I will retry with the -e flag and also by mounting both the input and output drives with the -B argument. So I will use something like the following:

-e -B /scratch1/sinha/ECDMT10000/derivatives \
-e -B /data/nil-external/ccp/XCP-D/xcp_sample_output_feb03-2025 \

Temporary since I will still have to explore processing DCAN type input data later on. I will have to find input datasets that are suitable for this purpose and not preprocessed using fMRIprep, unlike the one I am currently using.

I copied the full traceback message right from the beginning of my command to a .txt file. I tried uploading it but it says “Sorry, new users can not upload attachments.” I can paste it here but it is thousands of lines.

It does generate output files but it is missing some sub-folders. For instance, I could not locate the fmap sub-folder.

Thanks,
Saptarshi

Steven · February 4, 2025, 12:13am

Hi @ssinha,

No, you only need one instance of -e. Do you see any more log that actually has the specific error traceback? XCP_D does output any fmap derivatives: Outputs of XCP-D — xcp_d 0.10.5.dev18+g5c7821a documentation

Best,
Steven

ssinha · February 4, 2025, 7:32pm

Hello Steven,

I just wanted to let you know that I will be running a new trial with a single instance of the -e flag (like the sample below) and will let you know if I encounter the error again.

-e -B /scratch1/sinha/ECDMT10000/derivatives \
-B /data/nil-external/ccp/XCP-D/xcp_sample_output \

The error message that I encountered was generated at the very last stage of the XCP-D processing which I pasted earlier. I will go through the full traceback log and see if there are any other error messages that I may have missed.

I was wondering if you meant XCP-D does not output any fmap derivatives. Let me know if this is correct.

Thanks,
Saptarshi

Steven · February 4, 2025, 8:00pm

Yes sorry I meant to say does not output fmap derivatives.