🐛Freesurfer output data skips reorientation #2200
Description
Describe the bug
Resources from ingress_freesurfer are skipping reorient and are used directly like in here.
Probably the Freesurfer data is also used without reorientation.
This causes the files ingressed to have different orientation and is incompatible with rest of the data causing alignment issues such as above.
To reproduce
Ingress Freesurfer output dir where the orientation of volumetric datas are in different orientation than specified in the CPAC config. desired-orientation. Run CPAC with pre-config abcd-options
Preconfig
- default
- abcd-options
- anat-only
- blank
- ccs-options
- fmriprep-options
- fx-options
- monkey
- monkey-ABCD
- ndmg
- nhp-macaque
- preproc
- rbc-options
- rodent
Custom pipeline configuration
No response
Run command
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Expected behavior
The masked image (desc-preproc_T1w) should appear correct.
Acceptance criteria
All freesurfer data properly reoriented to the common orientaion as specified in the config.
Screenshots
C-PAC version
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Container platform
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Docker and/or Singularity version(s)
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Additional context
No response