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Fixes

Fixes #2184 by @birajstha

Description

Restores

"pipeline-fs_hemi-L_desc-surface_curv",
"pipeline-fs_hemi-R_desc-surface_curv",
"pipeline-fs_hemi-L_desc-surfaceMesh_pial",
"pipeline-fs_hemi-R_desc-surfaceMesh_pial",
"pipeline-fs_hemi-L_desc-surfaceMesh_smoothwm",
"pipeline-fs_hemi-R_desc-surfaceMesh_smoothwm",
"pipeline-fs_hemi-L_desc-surfaceMesh_sphere",
"pipeline-fs_hemi-R_desc-surfaceMesh_sphere",
"pipeline-fs_hemi-L_desc-surfaceMap_sulc",
"pipeline-fs_hemi-R_desc-surfaceMap_sulc",
"pipeline-fs_hemi-L_desc-surfaceMap_thickness",
"pipeline-fs_hemi-R_desc-surfaceMap_thickness",
"pipeline-fs_hemi-L_desc-surfaceMap_volume",
"pipeline-fs_hemi-R_desc-surfaceMap_volume",
"pipeline-fs_hemi-L_desc-surfaceMesh_white",
"pipeline-fs_hemi-R_desc-surfaceMesh_white",
(removed in #2184) to the outputs of
@nodeblock(
name="freesurfer_reconall",

Technical details

  • "freesurfer_reconall" includes all outputs of "freesurfer_abcd_preproc", so when these outputs were removed from "freesurfer_abcd_preproc", they were also removed from "freesurfer_reconall", which led to some failing smoke tests (see Screenshots for an example).
  • Also replaces the setup-conda GitHub Workflows Marketplace Action (the one that was there stopped working and hasn't been updated in a while).

Screenshots

NameError: [!] Output name "pipeline-fs_hemi-L_desc-surface_curv" in the block function does not match the outputs list ['freesurfer-subject-dir', 'pipeline-fs_raw-average', 'pipeline-fs_subcortical-seg', 'pipeline-fs_brainmask', 'pipeline-fs_wmparc', 'pipeline-fs_T1', 'desc-restore_T1w', 'desc-restore-brain_T1w', 'desc-ABCDpreproc_T1w', 'pipeline-fs_desc-fast_biasfield'] in Node Block "freesurfer_reconall"

smoke tests succeed

Checklist

  • My pull request has a descriptive title (not a vague title like Update index.md).
  • My pull request targets the develop branch of the repository.
  • My commit messages follow best practices.
  • My code follows the established code style of the repository.
  • I added tests for the changes I made (if applicable).
  • I updated the changelog.
  • I added or updated documentation (if applicable).
  • I tried running the project locally and verified that there are no visible errors.

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(a) The contribution was created in whole or in part by me and I
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(b) The contribution is based upon previous work that, to the best
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@birajstha birajstha left a comment

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Thanks for the fix

@shnizzedy shnizzedy merged commit 25d1bbd into develop Mar 3, 2025
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3 participants