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

Software Support
12

It looks like your fMRIPrep derivatives are missing transforms to and from MNI152NLin6Asym. Here are a few things that XCP-D needs that appear to be missing:

  1. Native anatomical-space T1w or T2w NIfTI (e.g., sub-<label>/anat/sub-<label>_desc-preproc_T1w.nii.gz).
  2. Native anatomical-space brain mask (e.g., sub-<label>/anat/sub-<label>_desc-brain_mask.nii.gz).
    • EDIT: Sorry about that- this needs to be in MNI152NLin6Asym, not native anatomical space.
  3. Transforms between native anatomical space and MNI152NLin6Asym space:
    • sub-<label>/anat/sub-<label>_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
    • sub-<label>/anat/sub-<label>_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
  4. Preprocessed BOLD data in MNI152NLin6Asym space.
  5. BOLD-reference image in MNI152NLin6Asym space.
13

Thanks for this.

It seems like I do have the required anat files:

"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-aparcaseg_dseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-aseg_dseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-brain_mask.json"@
**"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-brain_mask.nii.gz"@**
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-preproc_T1w.json"@
**"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-preproc_T1w.nii.gz"@**
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_dseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-fsnative_to-T1w_mode-image_xfm.txt"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5"@
**"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5"@**
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-fsnative_mode-image_xfm.txt"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"@
**"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5"@**
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_curv.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_inflated.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_midthickness.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_pial.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_smoothwm.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_sulc.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_thickness.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_curv.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_inflated.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_midthickness.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_pial.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_smoothwm.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_sulc.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_thickness.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_label-CSF_probseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_label-GM_probseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_label-WM_probseg.nii.gz"@

However in my func file, I seem to be missing Preprocessed BOLD data in MNI152NLin6Asym space and BOLD-reference image in MNI152NLin6Asym space (although I have AROMA output in this space).

"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_AROMAnoiseICs.csv"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_boldref.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-brain_mask.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-brain_mask.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-MELODIC_mixing.tsv"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-preproc_bold.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-preproc_bold.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_from-scanner_to-boldref_mode-image_xfm.txt"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_from-scanner_to-T1w_mode-image_xfm.txt"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_from-T1w_to-scanner_mode-image_xfm.txt"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_hemi-L_space-fsaverage5_bold.func.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_hemi-L_space-fsaverage5_bold.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_hemi-R_space-fsaverage5_bold.func.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_hemi-R_space-fsaverage5_bold.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.dtseries.nii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_bold.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz"@

Is there a way around this or would I need to rerun fmriprep to include the missing BOLD files you have mentioned?

14

The MNI152NLin6Asym BOLD files are just used for figures. You could probably symlink the following:

  • sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz → sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
  • sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json → sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-preproc_bold.json (this one might not actually be necessary- not sure)

You’ll need a 3D image for the boldref though. You could just grab the first volume of sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz and name it sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-MNI152NLin6Asym_boldref.nii.gz

15

Thank you very much for your suggestions. I have created the symlink named as MNI152NLin6Asym BOLD as well as the boldref 3D image.

I have run the XCP-D command with --input-type 'dcan' and still get FileNotFoundError: No BOLD data found in allowed spaces (fsLR).

But I then tried with --input-type 'fmriprep' (which is what would be correct/would make sense to begin with) and this seems to work. Now get the new error FileNotFoundError: No anat_brainmask found with query: {'datatype': 'anat', 'desc': 'brain', 'extension': '.nii.gz', 'suffix': 'mask', 'space': 'MNI152NLin6Asym'}.

As a reminder, here are the contents of my anat file:

"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-aparcaseg_dseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-aseg_dseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-brain_mask.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-brain_mask.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-preproc_T1w.json"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-preproc_T1w.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_dseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-fsnative_to-T1w_mode-image_xfm.txt"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-fsnative_mode-image_xfm.txt"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_curv.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_inflated.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_midthickness.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_pial.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_smoothwm.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_sulc.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-L_thickness.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_curv.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_inflated.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_midthickness.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_pial.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_smoothwm.surf.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_sulc.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_hemi-R_thickness.shape.gii"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_label-CSF_probseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_label-GM_probseg.nii.gz"@
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_label-WM_probseg.nii.gz"@

As pointed out by the error, I am indeed missing a mask in MNI152NLin6Asym space (mentioned as minimal inputs for CIFTI processing in the XCP-D docs):

  • sub-x_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
  • sub-x_space-MNI152NLin6Asym_desc-brain_mask.json

But I have the native anatomical space T1 NIfTI and mask, as well ask the transforms between native anatomical space and MNI152NLin6Asym space, which you’ve mentioned in your previous message.

Would there be a way around the MNI152NLin6Asym mask, or a way to obtain it without needing to rerun fmriprep? The type of workaround you have suggested for the missing BOLD files in MNI152NLin6Asym space (ie creating symlinks to existing similar files) does not seem to be appropriate in this case/with the currently available files in my directory…

Thank you very much in advance.

16

Hi @biancaserio,

You can apply your T1w-to-MNI transform to your mask to get the MNI mask.

E.g.,

antsApplyTransform \
-d 3 \
-i $SUB_MASK # e.g, sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_desc-brain_mask.nii.gz \
-r $MNIREF # e.g., an MNI152NLin6Asym file from templateflow 
-n NearestNeighbor # Since this is a binary mask file
-t $T1w_TO_MNI152NLin6Asym_XFM # e.g, sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
-o $OUTPUT # e.g., sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz

Best,
Steven

17

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'
18

Yes, that’s a bug that another user detected recently. The problem comes from using --file-format cifti + --linc-qc n + --abcc-qc n. I have it fixed in a recent PR, but I don’t think I’ve made a new release yet. In the meantime, the easiest workaround would be to switch to --linc-qc y.

19

Thank you very much @tsalo , I was now able to have XCP-D run without errors through to completion of this single subject.

I have some outstanding questions about the output, if that’s ok:

  1. I was expecting output for 4 runs, but I only see output for run1:
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_design.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_design.tsv"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_motion.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_motion.tsv"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_outliers.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_outliers.tsv"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_desc-denoised_bold.dtseries.nii"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_desc-denoised_bold.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_desc-denoisedSmoothed_bold.dtseries.nii"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_desc-denoisedSmoothed_bold.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_desc-linc_qc.tsv"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_stat-alff_boldmap.dscalar.nii"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_stat-alff_boldmap.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_stat-alff_desc-smooth_boldmap.dscalar.nii"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_stat-alff_desc-smooth_boldmap.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_stat-reho_boldmap.dscalar.nii"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_den-91k_stat-reho_boldmap.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_den-91k_stat-coverage_boldmap.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_den-91k_stat-coverage_boldmap.pscalar.nii"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_den-91k_stat-mean_timeseries.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_den-91k_stat-mean_timeseries.ptseries.nii"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-alff_bold.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-alff_bold.tsv"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-coverage_bold.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-coverage_bold.tsv"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-mean_timeseries.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-mean_timeseries.tsv"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-reho_bold.json"
"sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_stat-reho_bold.tsv"

This is despite the fact that the xcp_d.toml file in the /log folder includes: layout = "BIDS Layout: ...ta/ABCD/ABCD_fMRIprep/fmriprep | Subjects: 1 | Sessions: 1 | Runs: 4" , therefore recognizing the 4 runs. For your information, in my bids_filter_file.json, I did not specify a specific run. Could you please indicate where I could look for an explanation for the missing runs?

  1. I was expecting correlation matrices in the output and do not see any. I had specified --create-matrices 300 in my command, however the xcp_d.toml file includes the following: output_correlations = false , yet recognises dcan_correlation_lengths = [ 300.0,]. Should I have requested the creation of correlation matrices in a different way?

Full contents of the xcp_d.toml file:

[environment]
cpu_count = 32
exec_env = "posix"
free_mem = 549.5
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.8.6"
templateflow_version = "24.2.2"
version = "0.10.0rc3"

[execution]
fmri_dir = "/data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep"
aggr_ses_reports = 4
bids_database_dir = "/data/pt_02667/data/ABCD/work/20241117-164533_0654463c-ec21-4c4c-b9cb-e521e46c0c3e/bids_db"
bids_description_hash = "de1306035c3231fcdf2277f3288006d6dfa7b6814e448d1b75582a725173abfe"
boilerplate_only = false
confounds_config = "/data/pt_02667/data/ABCD/bianca/custom_confounds_24P_csf_wm.yaml"
debug = []
layout = "BIDS Layout: ...ta/ABCD/ABCD_fMRIprep/fmriprep | Subjects: 1 | Sessions: 1 | Runs: 4"
log_dir = "/data/pt_02667/data/ABCD/XCP-D_output/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = false
reports_only = false
output_dir = "/data/pt_02667/data/ABCD/XCP-D_output"
atlases = [ "4S456Parcels",]
run_uuid = "20241117-164533_0654463c-ec21-4c4c-b9cb-e521e46c0c3e"
participant_label = [ "NDARINV00CY2MDM",]
templateflow_home = "/data/hu_serio/.cache/templateflow"
work_dir = "/data/pt_02667/data/ABCD/work"
write_graph = false

[workflow]
mode = "abcd"
file_format = "cifti"
dummy_scans = "auto"
input_type = "fmriprep"
despike = true
smoothing = 6.0
output_interpolated = true
output_correlations = false
combine_runs = false
motion_filter_order = 4
head_radius = 50.0
fd_thresh = 0.3
min_time = 240.0
bandpass_filter = true
high_pass = 0.01
low_pass = 0.08
bpf_order = 2
min_coverage = 0.5
dcan_correlation_lengths = [ 300.0,]
process_surfaces = false
abcc_qc = false
linc_qc = true

[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 36
omp_nthreads = 1
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = false

[seeds]
master = 63555

[execution.datasets]
xcpdatlases = "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases"
xcpd4s = "/AtlasPack"

[execution.dataset_links]
preprocessed = "/data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep"
templateflow = "/data/hu_serio/.cache/templateflow"
atlas = "/data/pt_02667/data/ABCD/XCP-D_output/atlases"
xcpdatlases = "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases"
xcpd4s = "/AtlasPack"

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

[execution.bids_filters.bold]
session = [ "baselineYear1Arm1",]
task = [ "rest",]
space = [ "fsLR",]

Thank you very much in advance.

20

Can you share the stdout and stderr files from your run?

21

Thank you for asking to check those files (and apologies for not doing this myself to begin with, I’m quite new to this). Form the stderr output it looks like for runs 2-4, less than 240s survive the high-motion outlier scrubbing and for this reason the runs are not processed further. I don’t recognize an error message relating to the non-computation of connectivity matrices for run1 - but I imagine this must be because run1 only includes 251s, and I specified --create-matrices 300.

On another point, I was surprised to see that for run1 the size of the sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_space-fsLR_seg-4S456Parcels_den-91k_stat-mean_timeseries.ptseries.nii file is (383, 456), because the full timeseries (before removing any motion or dummy volumes) should be 383 for this run, yet I see the line in stderr: Found 5 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv. I thought that including the --dumy-scans flag would automatically remove the dummy volumes?

Thank you for all your time and support, I really appreciate it.

stdout:

241117-21:55:40,445 nipype.workflow IMPORTANT:
	 Running XCP-D version 0.10.0rc3
241117-21:55:40,446 nipype.workflow WARNING:
	 Previous output generated by version 0+unknown found.
241117-21:55:40,717 nipype.workflow IMPORTANT:
	 Building XCP-D's workflow:
           * Preprocessing derivatives path: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep.
           * Participant list: ['NDARINV00CY2MDM'].
           * Run identifier: 20241117-215529_f9cf607a-596c-4183-aeaf-116c49fc5bc2.
           * Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
241117-21:55:41,178 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

241117-21:55:41,242 nipype.utils INFO:
	 No standard-space surfaces found.
241117-21:55:41,349 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

241117-21:55:41,559 nipype.utils IMPORTANT:
	 Collected morphometry files:
cortical_thickness: null
cortical_thickness_corr: null
myelin: null
myelin_smoothed: null
sulcal_curv: null
sulcal_depth: null

241117-21:55:41,559 nipype.utils WARNING:
	 GeneratedBy key DNE: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/dataset_description.json. Using partial info.
241117-21:55:41,689 nipype.workflow INFO:
	 Loading atlas: 4S456Parcels
241117-21:55:43,737 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

Not required: xcpdatlases
Not required: xcpd4s
241117-21:55:43,796 nipype.utils INFO:
	 Found 5 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv
241117-21:55:43,813 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 ([]).
241117-21:55:44,347 nipype.utils IMPORTANT:
	 Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_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-02_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-02_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-02_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-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

Not required: xcpdatlases
Not required: xcpd4s
241117-21:55:44,397 nipype.utils INFO:
	 Found 4 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_desc-confounds_timeseries.tsv
241117-21:55:44,412 nipype.workflow WARNING:
	 Less than 240.0 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing (212.8). This run will not be processed.
241117-21:55:44,503 nipype.utils IMPORTANT:
	 Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_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-03_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-03_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-03_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-03_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

Not required: xcpdatlases
Not required: xcpd4s
241117-21:55:44,548 nipype.utils INFO:
	 Found 6 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_desc-confounds_timeseries.tsv
241117-21:55:44,559 nipype.workflow WARNING:
	 Less than 240.0 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing (120.0). This run will not be processed.
241117-21:55:44,782 nipype.utils IMPORTANT:
	 Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_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-04_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-04_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-04_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-04_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

Not required: xcpdatlases
Not required: xcpd4s
241117-21:55:44,827 nipype.utils INFO:
	 Found 4 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_desc-confounds_timeseries.tsv
241117-21:55:44,838 nipype.workflow WARNING:
	 Less than 240.0 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing (76.80000000000001). This run will not be processed.
241117-21:55:48,84 nipype.workflow INFO:
	 XCP-D workflow graph with 135 nodes built successfully.
241117-21:55:55,621 nipype.workflow IMPORTANT:
	 XCP-D started!
241117-21:56:01,98 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.ds_report_summary" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/ds_report_summary".
241117-21:56:01,205 nipype.workflow INFO:
	 [Node] Executing "ds_report_summary" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:01,213 nipype.workflow INFO:
	 [Node] Finished "ds_report_summary", elapsed time 0.005113s.
241117-21:56:01,220 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.random_censor" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/prepare_confounds_wf/random_censor".
241117-21:56:01,221 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.random_censor".
241117-21:56:01,246 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_anat_wf.ds_t1w_std" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_anat_wf/ds_t1w_std".
241117-21:56:01,312 nipype.workflow INFO:
	 [Node] Executing "ds_t1w_std" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:01,326 nipype.workflow INFO:
	 [Node] Executing "random_censor" <xcp_d.interfaces.censoring.RandomCensor>
241117-21:56:01,329 nipype.workflow INFO:
	 [Node] Finished "random_censor", elapsed time 0.00217s.
241117-21:56:03,624 nipype.workflow INFO:
	 [Node] Finished "ds_t1w_std", elapsed time 2.308893s.
241117-21:56:03,921 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_design_matrix" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/prepare_confounds_wf/ds_report_design_matrix".
241117-21:56:03,922 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_design_matrix".
241117-21:56:04,0 nipype.workflow INFO:
	 [Node] Executing "ds_report_design_matrix" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:04,12 nipype.workflow INFO:
	 [Node] Finished "ds_report_design_matrix", elapsed time 0.010862s.
241117-21:56:05,620 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_censoring" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/prepare_confounds_wf/ds_report_censoring".
241117-21:56:05,621 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_censoring".
241117-21:56:05,700 nipype.workflow INFO:
	 [Node] Executing "ds_report_censoring" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:05,715 nipype.workflow INFO:
	 [Node] Finished "ds_report_censoring", elapsed time 0.010966s.
241117-21:56:08,128 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.postproc_derivatives_wf.ds_confounds" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/postproc_derivatives_wf/ds_confounds".
241117-21:56:08,210 nipype.workflow INFO:
	 [Node] Executing "ds_confounds" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:08,221 nipype.workflow INFO:
	 [Node] Finished "ds_confounds", elapsed time 0.010392s.
241117-21:56:12,514 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_preproc_qc_nipreps" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/qc_report_wf/ds_report_preproc_qc_nipreps".
241117-21:56:12,515 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_preproc_qc_nipreps".
241117-21:56:12,547 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_postproc_qc_nipreps" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/qc_report_wf/ds_report_postproc_qc_nipreps".
241117-21:56:12,547 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_postproc_qc_nipreps".
241117-21:56:12,553 nipype.workflow INFO:
	 [Node] Executing "ds_report_preproc_qc_nipreps" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:12,564 nipype.workflow INFO:
	 [Node] Finished "ds_report_preproc_qc_nipreps", elapsed time 0.009584s.
241117-21:56:12,580 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.alff_wf.ds_report_alff" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/alff_wf/ds_report_alff".
241117-21:56:12,580 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.alff_wf.ds_report_alff".
241117-21:56:12,618 nipype.workflow INFO:
	 [Node] Executing "ds_report_postproc_qc_nipreps" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:12,624 nipype.workflow INFO:
	 [Node] Executing "ds_report_alff" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:12,634 nipype.workflow INFO:
	 [Node] Finished "ds_report_alff", elapsed time 0.009266s.
241117-21:56:12,637 nipype.workflow INFO:
	 [Node] Finished "ds_report_postproc_qc_nipreps", elapsed time 0.014702s.
241117-21:56:13,965 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_qualitycontrol" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/qc_report_wf/ds_report_qualitycontrol".
241117-21:56:13,977 nipype.workflow INFO:
	 [Node] Executing "ds_report_qualitycontrol" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:13,988 nipype.workflow INFO:
	 [Node] Finished "ds_report_qualitycontrol", elapsed time 0.009352s.
241117-21:56:14,349 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_coverage" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/connectivity_wf/ds_report_coverage".
241117-21:56:14,350 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_coverage".
241117-21:56:14,388 nipype.workflow INFO:
	 [Node] Executing "ds_report_coverage" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:14,393 nipype.workflow INFO:
	 [Node] Finished "ds_report_coverage", elapsed time 0.004508s.
241117-21:56:17,917 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.cifti_reho_wf.ds_report_reho" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/cifti_reho_wf/ds_report_reho".
241117-21:56:17,917 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.cifti_reho_wf.ds_report_reho".
241117-21:56:17,969 nipype.workflow INFO:
	 [Node] Executing "ds_report_reho" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:17,982 nipype.workflow INFO:
	 [Node] Finished "ds_report_reho", elapsed time 0.012053s.
241117-21:56:17,983 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_alff" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/connectivity_wf/ds_report_alff".
241117-21:56:17,983 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_alff".
241117-21:56:18,36 nipype.workflow INFO:
	 [Node] Executing "ds_report_alff" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:18,47 nipype.workflow INFO:
	 [Node] Finished "ds_report_alff", elapsed time 0.009519s.
241117-21:56:22,225 nipype.workflow INFO:
	 [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_reho" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/connectivity_wf/ds_report_reho".
241117-21:56:22,226 nipype.workflow INFO:
	 [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_reho".
241117-21:56:22,267 nipype.workflow INFO:
	 [Node] Executing "ds_report_reho" <xcp_d.interfaces.bids.DerivativesDataSink>
241117-21:56:22,272 nipype.workflow INFO:
	 [Node] Finished "ds_report_reho", elapsed time 0.00455s.
241117-21:56:25,822 nipype.workflow IMPORTANT:
	 XCP-D finished successfully!
241117-21:56:25,829 nipype.workflow IMPORTANT:
	 Works derived from this XCP-D execution should include the boilerplate text found in /data/pt_02667/data/ABCD/XCP-D_output/logs/CITATION.md.
241117-21:56:25,835 nipype.utils WARNING:
	 DatasetType key not in /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/dataset_description.json. Assuming 'derivative'.
22

stderr:

2024-11-17 21:55:31,128 [ 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
2024-11-17 21:55:31,138 [ 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
2024-11-17 21:55:31,435 [ WARNING] A valid FreeSurfer license file is recommended. Set the FS_LICENSE environment variable or use the '--fs-license-file' flag.
2024-11-17 21:55:34,387 [ 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
2024-11-17 21:55:39,289 [ 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
2024-11-17 21:55:39,292 [ 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
2024-11-17 21:55:40,445 [IMPORTANT] Running XCP-D version 0.10.0rc3
2024-11-17 21:55:40,446 [ WARNING] Previous output generated by version 0+unknown found.
2024-11-17 21:55:40,717 [IMPORTANT] Building XCP-D's workflow:
           * Preprocessing derivatives path: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep.
           * Participant list: ['NDARINV00CY2MDM'].
           * Run identifier: 20241117-215529_f9cf607a-596c-4183-aeaf-116c49fc5bc2.
           * Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
2024-11-17 21:55:41,178 [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

2024-11-17 21:55:41,242 [    INFO] No standard-space surfaces found.
2024-11-17 21:55:41,349 [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

2024-11-17 21:55:41,559 [IMPORTANT] Collected morphometry files:
cortical_thickness: null
cortical_thickness_corr: null
myelin: null
myelin_smoothed: null
sulcal_curv: null
sulcal_depth: null

2024-11-17 21:55:41,559 [ WARNING] GeneratedBy key DNE: /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/dataset_description.json. Using partial info.
2024-11-17 21:55:41,689 [    INFO] Loading atlas: 4S456Parcels
2024-11-17 21:55:43,737 [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

2024-11-17 21:55:43,796 [    INFO] Found 5 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-01_desc-confounds_timeseries.tsv
2024-11-17 21:55:43,813 [ 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 ([]).
2024-11-17 21:55:44,347 [IMPORTANT] Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_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-02_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-02_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-02_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-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

2024-11-17 21:55:44,397 [    INFO] Found 4 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_desc-confounds_timeseries.tsv
2024-11-17 21:55:44,412 [ WARNING] Less than 240.0 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-02_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing (212.8). This run will not be processed.
2024-11-17 21:55:44,503 [IMPORTANT] Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_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-03_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-03_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-03_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-03_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

2024-11-17 21:55:44,548 [    INFO] Found 6 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_desc-confounds_timeseries.tsv
2024-11-17 21:55:44,559 [ WARNING] Less than 240.0 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-03_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing (120.0). This run will not be processed.
2024-11-17 21:55:44,782 [IMPORTANT] Collected run data for sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_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-04_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-04_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-04_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-04_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

2024-11-17 21:55:44,827 [    INFO] Found 4 dummy scans in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_desc-confounds_timeseries.tsv
2024-11-17 21:55:44,838 [ WARNING] Less than 240.0 seconds in sub-NDARINV00CY2MDM_ses-baselineYear1Arm1_task-rest_run-04_space-fsLR_den-91k_bold.dtseries.nii survive high-motion outlier scrubbing (76.80000000000001). This run will not be processed.
2024-11-17 21:55:46,805 [ 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
2024-11-17 21:55:46,809 [ 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
2024-11-17 21:55:48,084 [    INFO] XCP-D workflow graph with 135 nodes built successfully.
2024-11-17 21:55:52,507 [ 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
2024-11-17 21:55:52,511 [ 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
2024-11-17 21:55:54,972 [ 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
2024-11-17 21:55:55,621 [IMPORTANT] XCP-D started!
2024-11-17 21:56:00,332 [ 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
2024-11-17 21:56:00,335 [ 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
2024-11-17 21:56:00,474 [ 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
2024-11-17 21:56:00,477 [ 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
2024-11-17 21:56:01,098 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.ds_report_summary" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/ds_report_summary".
2024-11-17 21:56:01,205 [    INFO] [Node] Executing "ds_report_summary" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:01,213 [    INFO] [Node] Finished "ds_report_summary", elapsed time 0.005113s.
2024-11-17 21:56:01,220 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.random_censor" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/prepare_confounds_wf/random_censor".
2024-11-17 21:56:01,221 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.random_censor".
2024-11-17 21:56:01,246 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_anat_wf.ds_t1w_std" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_anat_wf/ds_t1w_std".
2024-11-17 21:56:01,312 [    INFO] [Node] Executing "ds_t1w_std" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:01,326 [    INFO] [Node] Executing "random_censor" <xcp_d.interfaces.censoring.RandomCensor>
2024-11-17 21:56:01,329 [    INFO] [Node] Finished "random_censor", elapsed time 0.00217s.
2024-11-17 21:56:03,624 [    INFO] [Node] Finished "ds_t1w_std", elapsed time 2.308893s.
2024-11-17 21:56:03,921 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_design_matrix" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/prepare_confounds_wf/ds_report_design_matrix".
2024-11-17 21:56:03,922 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_design_matrix".
2024-11-17 21:56:04,000 [    INFO] [Node] Executing "ds_report_design_matrix" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:04,012 [    INFO] [Node] Finished "ds_report_design_matrix", elapsed time 0.010862s.
2024-11-17 21:56:04,873 [ 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
2024-11-17 21:56:04,876 [ 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
2024-11-17 21:56:05,620 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_censoring" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/prepare_confounds_wf/ds_report_censoring".
2024-11-17 21:56:05,621 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.prepare_confounds_wf.ds_report_censoring".
2024-11-17 21:56:05,700 [    INFO] [Node] Executing "ds_report_censoring" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:05,715 [    INFO] [Node] Finished "ds_report_censoring", elapsed time 0.010966s.
2024-11-17 21:56:08,128 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.postproc_derivatives_wf.ds_confounds" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/postproc_derivatives_wf/ds_confounds".
2024-11-17 21:56:08,210 [    INFO] [Node] Executing "ds_confounds" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:08,221 [    INFO] [Node] Finished "ds_confounds", elapsed time 0.010392s.
2024-11-17 21:56:12,514 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_preproc_qc_nipreps" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/qc_report_wf/ds_report_preproc_qc_nipreps".
2024-11-17 21:56:12,515 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_preproc_qc_nipreps".
2024-11-17 21:56:12,547 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_postproc_qc_nipreps" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/qc_report_wf/ds_report_postproc_qc_nipreps".
2024-11-17 21:56:12,547 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_postproc_qc_nipreps".
2024-11-17 21:56:12,553 [    INFO] [Node] Executing "ds_report_preproc_qc_nipreps" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:12,564 [    INFO] [Node] Finished "ds_report_preproc_qc_nipreps", elapsed time 0.009584s.
2024-11-17 21:56:12,580 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.alff_wf.ds_report_alff" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/alff_wf/ds_report_alff".
2024-11-17 21:56:12,580 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.alff_wf.ds_report_alff".
2024-11-17 21:56:12,618 [    INFO] [Node] Executing "ds_report_postproc_qc_nipreps" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:12,624 [    INFO] [Node] Executing "ds_report_alff" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:12,634 [    INFO] [Node] Finished "ds_report_alff", elapsed time 0.009266s.
2024-11-17 21:56:12,637 [    INFO] [Node] Finished "ds_report_postproc_qc_nipreps", elapsed time 0.014702s.
2024-11-17 21:56:13,965 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.qc_report_wf.ds_report_qualitycontrol" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/qc_report_wf/ds_report_qualitycontrol".
2024-11-17 21:56:13,977 [    INFO] [Node] Executing "ds_report_qualitycontrol" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:13,988 [    INFO] [Node] Finished "ds_report_qualitycontrol", elapsed time 0.009352s.
2024-11-17 21:56:14,349 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_coverage" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/connectivity_wf/ds_report_coverage".
2024-11-17 21:56:14,350 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_coverage".
2024-11-17 21:56:14,388 [    INFO] [Node] Executing "ds_report_coverage" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:14,393 [    INFO] [Node] Finished "ds_report_coverage", elapsed time 0.004508s.
2024-11-17 21:56:17,917 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.cifti_reho_wf.ds_report_reho" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/cifti_reho_wf/ds_report_reho".
2024-11-17 21:56:17,917 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.cifti_reho_wf.ds_report_reho".
2024-11-17 21:56:17,969 [    INFO] [Node] Executing "ds_report_reho" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:17,982 [    INFO] [Node] Finished "ds_report_reho", elapsed time 0.012053s.
2024-11-17 21:56:17,983 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_alff" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/connectivity_wf/ds_report_alff".
2024-11-17 21:56:17,983 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_alff".
2024-11-17 21:56:18,036 [    INFO] [Node] Executing "ds_report_alff" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:18,047 [    INFO] [Node] Finished "ds_report_alff", elapsed time 0.009519s.
2024-11-17 21:56:22,225 [    INFO] [Node] Setting-up "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_reho" in "/data/pt_02667/data/ABCD/work/xcp_d_0_10_wf/sub_NDARINV00CY2MDM_wf/postprocess_0_wf/connectivity_wf/ds_report_reho".
2024-11-17 21:56:22,226 [    INFO] [Node] Outdated cache found for "xcp_d_0_10_wf.sub_NDARINV00CY2MDM_wf.postprocess_0_wf.connectivity_wf.ds_report_reho".
2024-11-17 21:56:22,267 [    INFO] [Node] Executing "ds_report_reho" <xcp_d.interfaces.bids.DerivativesDataSink>
2024-11-17 21:56:22,272 [    INFO] [Node] Finished "ds_report_reho", elapsed time 0.00455s.
2024-11-17 21:56:25,822 [IMPORTANT] XCP-D finished successfully!
2024-11-17 21:56:25,829 [IMPORTANT] Works derived from this XCP-D execution should include the boilerplate text found in /data/pt_02667/data/ABCD/XCP-D_output/logs/CITATION.md.
2024-11-17 21:56:25,835 [ WARNING] DatasetType key not in /data/pt_02667/data/ABCD/ABCD_fMRIprep/fmriprep/dataset_description.json. Assuming 'derivative'.
24

It looks like there’s a bug in XCP-D (sorry about that) with how output_correlations is set. I will push a fix in the morning, but you can work around it by changing --create-matrices 300 to --create-matrices 300 all.

The parcellated time series should be 5 volumes (the number of identified dummy volumes) shorter than the original time series length since abcd mode outputs interpolated time series.

25

Using --create-matrices 300 all works, thanks a lot!

Just to clarify, I think you meant that the parcellated timeseries should be shorter than the original timeseries when the --output-type is set to censored, whereas it should remain the same when the --output-type is set to interpolated (or auto in the abcd mode)?

The above is what I experienced by trying out the different parameters.

I also wanted to let you know that I run into the error '--output-type' cannot be 'censored' for 'abcd' mode. despite the fact that the documentation for XCP-D suggests that “Correlation matrices can be created optionally from the censored data.” I don’t know if this would require a different set/combination of parameters in the command (rather than just setting the '--output-type' cannot be 'censored' for 'abcd' mode.).

26

Dummy volumes are treated differently from motion outlier volumes. Let’s say you have a time series with 100 volumes, 5 of which are dummy volumes, and 10 of which are high-motion outlier volumes. With censored, you should have a time series with 85 volumes (100 - 5 - 10). With interpolated, you should have one with 95 volumes (100 - 5).

That refers to the correlation matrices. You never get correlation matrices from the interpolated data in XCP-D, regardless of what mode you use or output type you select. Even if the output type for the dense and parcellated time series is “interpolated”, your correlation matrices will still be created from the censored time series.

27

Thank you very much for this, it makes sense. Thank you @tsalo and @Steven for all you time and help, I really appreciate it!

28

Hi @tsalo,

I just wanted to get back to you with regard to the dummy volumes, as the output of XCP does not seem to correspond to what you have described (automatic exclusion of dummy volumes from the timeseries).

  • I have --dummy-scans set to 'auto'
  • According to stderr.log, run1 has 251s surviving high-motion outlier scrubbing, and has 5 dummy scans
  • My XCP-D output includes 318 points in its timeseries.

When trying to make sense of the number 318, I am considering that my data has been collected with a TR of 0.8s, therefore 251s/0.8s= 313 timepoints. This means that 318 (the XCP output timeseries length) includes the 5 dummy volumes.

Given that the exclusion of dummy volumes does not appear to be automatic, I was wondering if there is a specific flag that needs to be set in order to do this.

Thank you in advance.

29

You used “abcd” mode, right? If so, then the output timeseries has interpolated values in place of the high-motion volumes, so the length isn’t equal to the amount of time with low-motion data times the TR. I would recommend checking the preprocessed data to see how long the original run was, in terms of volumes.

30

I have actually now switched to --mode 'none' with --output-type 'censored', which is why I am expecting both dummy and high motion volumes to be removed. My preprocessed data has 383 volumes (306.4s).

For your information, this is the full command

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 'none' \
--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 'censored' \
--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 240 all \
--work-dir /data/pt_02667/data/ABCD/work \
--warp-surfaces-native2std 'n' \
--abcc-qc 'n' \
--linc-qc 'y' \
1> /data/pt_02667/data/ABCD/work/stdout.log 2> /data/pt_02667/data/ABCD/work/stderr.log
31

Okay, I think I understand the problem. You’re 100% right that the time series should be 5 volumes shorter. It looks like I introduced a bug in 0.10.0rc1 where the dummy volumes were not being inferred from the right file at the point in the post-processing workflow where they’re actually used. I am pushing a fix now and I’ll release 0.10.1 in a couple of hours.

32

Thank you very much!