🐛 Add reorientation to the Freesurfer outputs when ran within CPAC.

[birajstha]

Describe the bug

Brought up by @shnizzedy in #2199

We added reorient to the .mgz files for Freesurfer ingress node. We will need to test and add this when Freesurfer is run natively in CPAC.

To reproduce

No response

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

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Run command

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Expected behavior

No weird masking of the final desc-preproc when using abcd and ccs preconfig with freesurfer recon-all running natively within CPAC.

Acceptance criteria

• reorientation added to .mgz files when adding resources to the pool.
• CCS preconfig, particularly brain-masking using: Freesurfer-Brainmask shows no weird masking behavior.

Screenshots

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C-PAC version

No response

Container platform

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Docker and/or Singularity version(s)

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Additional context

No response