Thank you @Steven, this is really helpful.
It seems that the preprocessing now starts, however halting after this output:
2024-11-16 22:32:23,273 [ 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
2024-11-16 22:32:23,280 [ 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
2024-11-16 22:32:23,580 [ WARNING] A valid FreeSurfer license file is recommended. Set the FS_LICENSE environment variable or use the '--fs-license-file' flag.
2024-11-16 22:32:26,633 [ 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
2024-11-16 22:32:32,344 [ 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
2024-11-16 22:32:32,347 [ 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
241116-22:32:33,402 nipype.workflow IMPORTANT:
Running XCP-D version 0.10.0rc3
2024-11-16 22:32:33,402 [IMPORTANT] Running XCP-D version 0.10.0rc3
241116-22:32:33,643 nipype.workflow IMPORTANT:
Building XCP-D's workflow:
* Preprocessing derivatives path: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep.
* Participant list: ['NDARINV00CY2MDM'].
* Run identifier: 20241116-223221_60c7288e-05a3-4811-9192-a69f188b7e58.
* Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
2024-11-16 22:32:33,643 [IMPORTANT] Building XCP-D's workflow:
* Preprocessing derivatives path: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep.
* Participant list: ['NDARINV00CY2MDM'].
* Run identifier: 20241116-223221_60c7288e-05a3-4811-9192-a69f188b7e58.
* Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
241116-22:32:34,251 nipype.utils IMPORTANT:
Collected data:
anat_brainmask: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
anat_to_template_xfm: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
bold:
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.dtseries.nii
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_space-fsLR_den-91k_bold.dtseries.nii
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_space-fsLR_den-91k_bold.dtseries.nii
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_space-fsLR_den-91k_bold.dtseries.nii
t1w: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-preproc_T1w.nii.gz
t2w: null
template_to_anat_xfm: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
2024-11-16 22:32:34,251 [IMPORTANT] Collected data:
anat_brainmask: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
anat_to_template_xfm: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
bold:
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.dtseries.nii
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_space-fsLR_den-91k_bold.dtseries.nii
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_space-fsLR_den-91k_bold.dtseries.nii
- /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_space-fsLR_den-91k_bold.dtseries.nii
t1w: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-preproc_T1w.nii.gz
t2w: null
template_to_anat_xfm: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
241116-22:32:34,325 nipype.utils INFO:
No standard-space surfaces found.
2024-11-16 22:32:34,325 [ INFO] No standard-space surfaces found.
241116-22:32:34,548 nipype.utils IMPORTANT:
Collected mesh files:
lh_pial_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_pial.surf.gii
lh_subject_sphere: null
lh_wm_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_smoothwm.surf.gii
rh_pial_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_pial.surf.gii
rh_subject_sphere: null
rh_wm_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_smoothwm.surf.gii
2024-11-16 22:32:34,548 [IMPORTANT] Collected mesh files:
lh_pial_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_pial.surf.gii
lh_subject_sphere: null
lh_wm_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_smoothwm.surf.gii
rh_pial_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_pial.surf.gii
rh_subject_sphere: null
rh_wm_surf: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/anat/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_smoothwm.surf.gii
241116-22:32:34,644 nipype.utils IMPORTANT:
Collected morphometry files:
cortical_thickness: null
cortical_thickness_corr: null
myelin: null
myelin_smoothed: null
sulcal_curv: null
sulcal_depth: null
2024-11-16 22:32:34,644 [IMPORTANT] Collected morphometry files:
cortical_thickness: null
cortical_thickness_corr: null
myelin: null
myelin_smoothed: null
sulcal_curv: null
sulcal_depth: null
241116-22:32:34,644 nipype.utils WARNING:
GeneratedBy key DNE: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/dataset_description.json. Using partial info.
2024-11-16 22:32:34,644 [ WARNING] GeneratedBy key DNE: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/dataset_description.json. Using partial info.
241116-22:32:34,777 nipype.workflow INFO:
Loading atlas: 4S456Parcels
2024-11-16 22:32:34,777 [ INFO] Loading atlas: 4S456Parcels
241116-22:32:36,992 nipype.utils IMPORTANT:
Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.dtseries.nii:
boldref: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_boldref.nii.gz
motion_file: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv
motion_json: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.json
nifti_file: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
2024-11-16 22:32:36,992 [IMPORTANT] Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.dtseries.nii:
boldref: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_boldref.nii.gz
motion_file: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv
motion_json: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.json
nifti_file: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/sub-NDARINV00CY2MDM/ses-baselineYear1Arm1/func/sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
Not required: xcpdatlases
Not required: xcpd4s
241116-22:32:37,52 nipype.utils INFO:
Found 5 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv
2024-11-16 22:32:37,052 [ INFO] Found 5 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv
241116-22:32:37,68 nipype.utils WARNING:
251.20000000000002 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing. Only retaining exact-time values greater than this ([]).
2024-11-16 22:32:37,068 [ WARNING] 251.20000000000002 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing. Only retaining exact-time values greater than this ([]).
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 469, in init_single_subject_wf
postprocess_bold_wf = init_postprocess_bold_wf(
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/bold/cifti.py", line 301, in init_postprocess_cifti_wf
workflow.connect([
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 239, in connect
raise Exception("\n".join(["Some connections were not found"] + infostr))
Exception: Some connections were not found
Module qc_report_wf has no input called inputnode.name_source
Module qc_report_wf has no input called inputnode.preprocessed_bold
Module qc_report_wf has no input called inputnode.dummy_scans
Module qc_report_wf has no input called inputnode.motion_file
Module qc_report_wf has no input called inputnode.temporal_mask
Module qc_report_wf has no input called inputnode.denoised_interpolated_bold
Module qc_report_wf has no input called inputnode.censored_denoised_bold
I found an issue on the Xcp_d: Some connections were not found problem, although in my case this does not seem to relate to surface files but rather to outputs of the XCP-D post-processing pipeline itself? I would be very grateful to get your thoughts on this - thank you in advance.
Note: I am using the following command/parameters:
singularity run \
-B /data/pt_02667/data/ABCD:/data/pt_02667/data/ABCD \
--cleanenv /data/u_serio_software/xcp_d-0.10.0rc3.simg \
/data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep \
/data/pt_02667/data/ABCD/XCP-D_output \
participant \
--mode 'abcd' \
--participant-label 'NDARINV00CY2MDM' \
--bids-filter-file /data/pt_02667/data/ABCD/bianca/bids_filter_file.json \
--nprocs 36 \
--input-type 'fmriprep' \
--file-format 'cifti' \
--dummy-scans 'auto' \
--despike 'y' \
--nuisance-regressors /data/pt_02667/data/ABCD/bianca/custom_confounds_24P_csf_wm.yaml \
--fd-thresh 0.3 \
--output-type 'auto' \
--combine-runs 'n' \
--smoothing 6 \
--motion-filter-type 'none' \
--head-radius 50 \
--lower-bpf 0.01 \
--upper-bpf 0.08 \
--bpf-order 2 \
--min-time 240 \
--atlases '4S456Parcels' \
--min-coverage 0.5 \
--create-matrices 300 \
--work-dir /data/pt_02667/data/ABCD/work \
--warp-surfaces-native2std 'n' \
--abcc-qc 'n' \
--linc-qc 'n'