Hello Steven,
Many thanks for your quick response! I deeply appreciate the support. I should have added some more information in my original email, but will provide them now and also try to address your queries.
Regarding the input data that I am using, I did not pre-process it myself but it was conducted by my colleagues at the Cognitive Control & Psychopathology Laboratory in Washington University in St. Louis as part of the ECDMT project. I believe my colleagues used fMRIprep pipelines for preprocessing.
Regarding the extra arguments, thank you for letting me know about the invalidity of the “--exact-time 300 480 600” argument. Is it the same case with the “--dcan-qc” argument? The only options I could find were those involving “--linc-qc” and “--abcc-qc”, but not about “--dcan-qc” in the documentation. We obtained these extra arguments from our UPenn associates.
Regarding the FileNotFoundError, I referred to an earlier post in this forum regarding this issue and also the marked solution. It appears that the required files are present in the directory. Here are the observations I made:
sinhas@ccplinux1% ls *desc-preproc_T1w.nii.gz -l
-rw-r--r--+ 1 sinhas input 56098408 Dec 16 03:02 sub-ECDMT10000_ses-1_desc-preproc_T1w.nii.gz
-rw-r--r--+ 1 sinhas input 15258395 Dec 16 03:01 sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
-rw-r--r--+ 1 sinhas input 957005 Dec 16 03:02 sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
sinhas@ccplinux1% ls *desc-brain_mask.nii.gz -l
-rw-r--r--+ 1 sinhas input 86094 Dec 16 03:01 sub-ECDMT10000_ses-1_desc-brain_mask.nii.gz
-rw-r--r--+ 1 sinhas input 92203 Dec 16 03:02 sub-ECDMT10000_ses-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
-rw-r--r--+ 1 sinhas input 10785 Dec 16 03:01 sub-ECDMT10000_ses-1_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
sinhas@ccplinux1% ls *from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5 -l
-rw-r--r--+ 1 sinhas input 74500580 Dec 16 03:01 sub-ECDMT10000_ses-1_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
sinhas@ccplinux1% ls *from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5 -l
-rw-r--r--+ 1 sinhas input 74503278 Dec 16 03:02 sub-ECDMT10000_ses-1_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
sinhas@ccplinux1% pwd
/data/nil-external/ccp/XCP-D/ECDMT10000/derivatives/sub-ECDMT10000/ses-1/anat
Regarding the the traceback error, here is a snippet for your reference:
250127-19:35:24,355 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
2025-01-27 19:35:24,355 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t1w_on_atlas_wf.plot_overlay_figure
250127-19:35:24,368 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
2025-01-27 19:35:24,368 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t1w_wf.plot_overlay_figure
250127-19:35:24,379 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,379 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250127-19:35:24,388 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-01-27 19:35:24,388 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250127-19:35:24,396 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,396 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t1w_on_task_wf.plot_overlay_figure
250127-19:35:24,403 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
2025-01-27 19:35:24,403 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t1w_wf.plot_overlay_figure
250127-19:35:24,411 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
2025-01-27 19:35:24,411 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_t2w_on_atlas_wf.plot_overlay_figure
250127-19:35:24,418 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,418 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_anat_wf.execsummary_anatomical_plots_wf.plot_atlas_on_t2w_wf.plot_overlay_figure
250127-19:35:24,426 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,426 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250127-19:35:24,433 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,433 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_0_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
250127-19:35:24,441 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
2025-01-27 19:35:24,441 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_t2w_on_task_wf.plot_overlay_figure
250127-19:35:24,449 nipype.workflow ERROR:
could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,449 [ ERROR] could not run node: xcp_d_0_10_wf.sub_ECDMT10000_wf.postprocess_1_wf.execsummary_functional_plots_wf.plot_task_on_t2w_wf.plot_overlay_figure
2025-01-27 19:35:24,549 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,563 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,573 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,583 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,593 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,603 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,612 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,622 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,632 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,642 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,651 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2025-01-27 19:35:24,662 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
250127-19:35:24,687 nipype.workflow CRITICAL:
XCP-D failed: 12 raised. Re-raising first.
2025-01-27 19:35:24,687 [CRITICAL] XCP-D failed: 12 raised. Re-raising first.
2025-01-27 19:35:42,865 [ WARNING] WARNING: The 'strip_cdata' option of HTMLParser() has never done anything and will eventually be removed.
sinhas@ccplinux1%
Thanks again for your support!
Saptarshi