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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 E chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au http://secure-web.cisco.com/1xDAoEUxMPPuCsJFESgxVj8G_Fqd-g7vRsh53KrQ6HSMvkl4...http://secure-web.cisco.com/17tnfb4NVhmhEj8eHc-vz41g2VE4LFjxQeJHBYmM2X28ZojsWwRAdx4GxPhILKEZ_DbxWdmDXo1MEomx07dI5SXGgBBpivrkZXsRnh-NmfjN4jGpewAU_XWcMkC5_r-xLOYXnFQiN-PIozcA4rrxOt3LX9outyK7w8P6mCA_QzpV-F2g_Bsff69AhBjc8yWwsE4GkSKdTM4RS2AQlU2bkEyv8Sjov66mzFGPGx4_0ZEX8PJl-FzpfTYcpqnjxUta7cQpG1BaSXBXRL0aDJ3guDGCWvBxpPDKeVFyvt3HHPj-rSLxmxX7QblU_e6a31c8iYznfr7dut1Ek81_bNNuWHg/http%3A%2F%2Fwww.mcri.edu.au%2F

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