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

Software Support
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!