Fix/restore brain intensity abcd

[birajstha]

Fixes

Fixes #2206 by @birajstha
Related to #2047
Details are discussed here in the slack thread.

Description

Adds a specific switch for restore_t1w_intensity

Technical details

Tests

Tested running test-config.
It completed fine after the fix.

#!/usr/bin/bash
#SBATCH -N 1
#SBATCH -p RM-shared
#SBATCH -t 50:00:00

MED=/ocean/projects/med250004p
DATA=/ocean/projects/med250004p/bshresth/projects/fs_orientation/data
OUTPUT=/ocean/projects/med250004p/bshresth/projects/fs_orientation/output2
IMAGE=/ocean/projects/med250004p/bshresth/projects/fs_orientation/cpac_nightly.sif

PIPELINE=/ocean/projects/med250004p/bshresth/projects/fs_orientation/configs/ingress_fs.yml


subject=sub-PA001


repo=/ocean/projects/med250004p/bshresth/projects/fs_orientation/C-PAC
singularity run \
    -B $MED \
    -B $DATA:$DATA \
    -B $OUTPUT:$OUTPUT $IMAGE $DATA $OUTPUT test-config \
    --num_ants_threads 5 \
    --skip_bids_validator \
    --n_cpus 2 \
    --mem_gb 50 \
    --pipeline_file $PIPELINE \
    --participant_label $subject

Screenshots

Before

After the fix

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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[sgiavasis]

Looks great, thank you!!