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Don’t worry, figured it out with mris_transform.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Chris Adamson Sent: Monday, 1 June 2020 8:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer 7 long -> cross surfaces
External Email - Use Caution 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 E chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au www.mcri.edu.auhttp://www.mcri.edu.au/
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