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Added call to create jacobian_white measure directly in fastsurfer #282

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merged 2 commits into from
Apr 5, 2023
Merged

Added call to create jacobian_white measure directly in fastsurfer #282

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0fde348
Added call to create jacobian_white measure directly in fastsurfer
LeHenschel Apr 4, 2023
f7d5190
Jacobian needs surfreg - add check for it
LeHenschel Apr 4, 2023
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5 changes: 5 additions & 0 deletions recon_surf/recon-surf.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -884,6 +884,11 @@ else

echo "pushd $mdir" >> $CMDF
# these are run automatically in fs7* recon-all and cannot be called directly without -pial flag (or other t2 flags)
if [ "$fssurfreg" == "1" ] ; then
# jacobian needs sphere reg which might be turned off by user (on by default)
cmd="mris_jacobian ../surf/$hemi.white ../surf/$hemi.sphere.reg ../surf/$hemi.jacobian_white"
RunIt "$cmd" $LF $CMDF
fi
cmd="mris_place_surface --curv-map ../surf/$hemi.white 2 10 ../surf/$hemi.curv"
RunIt "$cmd" $LF $CMDF
cmd="mris_place_surface --area-map ../surf/$hemi.white ../surf/$hemi.area"
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