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Freesurfer experts,
I'm trying to make average surfaces for a collection of subjects into a template space. I have performed
the following flirt registration per subject:
flirt -in $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz -ref template0.nii.gz -omat
$SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat -out
$SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.nii.gz -dof 12 -searchrx -$D
$D -searchry -$D $D -searchrz -$D $D
Then make the talairach.xfm files for each subject
lta_convert --infsl $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat --outmni $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.xfm --src $SUBJECTS_DIR/$CURSUBJECT/mri/T2.mgz
–trg template0.nii.gz
Then run mris_make_average_surface
mris_make_average_surface -i 7 -s $CURSURFTYPE $CURHEMI $CURSURFTYPE.flirt sphere.reg2 fsaverage
The resulting average surface does not overlay onto
template0.nii.gz correctly, it is in the wrong orientation. It isn’t in TKR space, so I convert it to TKR space. mris_convert --vol-geom template0.nii.gz $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt.volgeom
mris_convert --vol-geom template0.nii.gz --to-tkr $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE.flirt.volgeom $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE
The resulting surface $SUBJECTS_DIR/fsaverage/surf/$CURHEMI.$CURSURFTYPE overlays onto the template template0.nii.gz but it is offset slightly and not overlaid
correctly. Am I doing something wrong?
Thanks in advance,
Chris.
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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