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I had a script that transformed volumes and surfaces from long (base) space back to cross space for comparison. It doesn’t work in Freesurfer 7 and I haven’t been able to figure out why. Volumes work with the same code but surfaces are
misaligned in cross space. The code is below, any thoughts on how to fix it?
Cheers.
SURFS="white
pial
inflated"
HEMIS="lh
rh"
cd $SUBJECTS_DIR/$LONG/surf
lta_convert --inlta $SUBJECTS_DIR/$BASE/mri/transforms/${CROSS}_to_${BASE}.lta --outreg register.native.dat --src $SUBJECTS_DIR/$CROSS/mri/rawavg.mgz
for CURHEMI in $HEMIS
do
for CURSURF in $SURFS
do
mri_surf2surf --sval-xyz $CURSURF --reg-inv register.native.dat --tval $SUBJECTS_DIR/$OUTDIR/surf/$CURHEMI.$CURSURF --tval-xyz $SUBJECTS_DIR/$CROSS/mri/rawavg.mgz --hemi $CURHEMI --s $LONG
done
done
Dr Chris Adamson
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road, Parkville, VIC 3052 Australia
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