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- #!/bin/bash
- set -e
- set -u
- subj=$1
- betopts="${2:--R -f 0.1 -g 0.0}"
- subjdir="${subj}/t1w"
- mkdir -p "${subjdir}"
- # this will produce the input to the freesurfer recon-all pipeline
- $FSLDIR/bin/fslreorient2std \
- raw/structural/$subj/anat/${subj}_T1w \
- ${subjdir}/head
- $FSLDIR/bin/bet \
- ${subjdir}/head \
- ${subjdir}/brain \
- -m ${betopts}
- mkdir -p "${subjdir}/in_mni152"
- $FSLDIR/bin/flirt -dof 12 \
- -in ${subjdir}/brain \
- -ref /usr/share/data/fsl-mni152-templates/MNI152_T1_1mm_brain.nii.gz \
- -omat "${subjdir}/in_mni152/subj2tmpl.mat" \
- -out "${subjdir}/in_mni152/brain"
- $FSLDIR/bin/convert_xfm \
- -omat "${subjdir}/in_mni152/tmpl2subj.mat" \
- -inverse "${subjdir}/in_mni152/subj2tmpl.mat"
- ## make the brain image's sform transform to MNI space
- #PYTHONPATH=code/ofhelpers python -c \
- # "import os; os.chdir(\"${subjdir}\"); from openfmri.nipype_helpers import update_sform2mni; update_sform2mni(\"brain.nii.gz\", \"in_mni152/subj2tmpl.mat\", \"/usr/share/data/fsl-mni152-templates/MNI152_T1_1mm_brain.nii.gz\")"
- #mv "${subjdir}/updated_sform.nii.gz" "${subjdir}/brain.nii.gz"
- $FSLDIR/bin/fast -n 3 -t 1 -g -B -p \
- -a "${subjdir}/in_mni152/tmpl2subj.mat" \
- -o "${subjdir}/brain" \
- "${subjdir}/brain"
- # rename FAST output
- mv "${subjdir}/brain_seg_0.nii.gz" "${subjdir}/brain_seg_csf.nii.gz"
- mv "${subjdir}/brain_seg_1.nii.gz" "${subjdir}/brain_seg_gray.nii.gz"
- mv "${subjdir}/brain_seg_2.nii.gz" "${subjdir}/brain_seg_white.nii.gz"
- mv "${subjdir}/brain_pve_0.nii.gz" "${subjdir}/brain_pve_csf.nii.gz"
- mv "${subjdir}/brain_pve_1.nii.gz" "${subjdir}/brain_pve_gray.nii.gz"
- mv "${subjdir}/brain_pve_2.nii.gz" "${subjdir}/brain_pve_white.nii.gz"
- mv "${subjdir}/brain_prob_0.nii.gz" "${subjdir}/brain_prob_csf.nii.gz"
- mv "${subjdir}/brain_prob_1.nii.gz" "${subjdir}/brain_prob_gray.nii.gz"
- mv "${subjdir}/brain_prob_2.nii.gz" "${subjdir}/brain_prob_white.nii.gz"
- mv "${subjdir}/brain_restore.nii.gz" "${subjdir}/brain_nobias.nii.gz"
- mv "${subjdir}/brain_gm_stdspace.nii.gz" "${subjdir}/brain_gray_stdspace.nii.gz"
- mv "${subjdir}/brain_wm_stdspace.nii.gz" "${subjdir}/brain_white_stdspace.nii.gz"
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