63 lines
1.8 KiB
Bash
Executable file
63 lines
1.8 KiB
Bash
Executable file
#!/bin/bash
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#
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# Usage: reg2std4feat <tntdir> <inspace> <stdspace> <feat_dir> [<feat_dir> ...]
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#
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# Example: reg2std4feat src/tnt/ bold3Tp2 grpbold3Tp2 sub-/run*_testme.feat
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#
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# This script makes the assumption that there is no highres space, but
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# alignment was performed from BOLD directly to a group template (most
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# likely computed from BOLD as well)
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#
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set -e
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set -u
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tntdir="$1"
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shift
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inspace="$1"
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shift
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stdspace="$1"
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shift
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for featdir in $@; do
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subj="$(echo $featdir| sed -e 's,.*\(sub-.*\)/.*,\1,g')"
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tntsubdir="${tntdir}/${subj}"
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# sane defaults
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tmpl2std_mat="$FSLDIR/etc/flirtsch/ident.mat"
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tmpl2std_warp=""
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# cleanup existing standard space registration
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[ -d "$featdir/reg_standard" ] && rm -rf "$featdir/reg_standard" || true
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# place reg info in existing featdir in a way that featregapply would
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# swallow it
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regdir="$featdir/reg"
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mkdir -p "$regdir"
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# remove any possibly existing standard space setup
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rm -rf "$regdir"/*standard*
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if [ "$inspace" != "$stdspace" ]; then
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xfmdir="$tntsubdir/$inspace/in_$stdspace"
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# check that we have the xfm info
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[ $(imtest "$xfmdir/head") -eq 1 ] && : || echo "cannot find transformation"
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if [ -e "$xfmdir/xfm_12dof.mat" ]; then
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tmpl2std_mat="$xfmdir/xfm_12dof.mat"
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fi
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if [ $(imtest "$xfmdir/subj2tmpl_warp") -eq 1 ]; then
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tmpl2std_warp="$xfmdir/subj2tmpl_warp"
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fi
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imcp "$xfmdir/head" "$regdir/standard"
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else
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# we stay in the
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imcp "$tntsubdir/$inspace/brain" "$regdir/standard"
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fi
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if [ -e "$regdir/example_func2highres.mat" ]; then
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convert_xfm -omat "$regdir/example_func2standard.mat" \
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-concat "$tmpl2std_mat" \
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"$regdir/example_func2highres.mat"
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else
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cp "$tmpl2std_mat" "$regdir/example_func2highres.mat"
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cp "$tmpl2std_mat" "$regdir/example_func2standard.mat"
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fi
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if [ -n "$tmpl2std_warp" ]; then
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imcp "$tmpl2std_warp" "$regdir/highres2standard_warp"
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fi
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done
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