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