Sometimes the volume orientation needs to be flipped to LPI, to match the surfaces. You can use either Freesurfer's mri_convert or AFNI's 3daxialize to do this.
Typically, the surface needs a translation to align with the orig volume, e.g.: ################################################# # Shift surface from Freesurfer space to orig ################################################# X_OFFSET=`$FREESURFER_DIR/bin/mri_info --cras ../mri/orig.LPI.nii | cut -f1 -d' '` Y_OFFSET=`$FREESURFER_DIR/bin/mri_info --cras ../mri/orig.LPI.nii | cut -f2 -d' '` Z_OFFSET=`$FREESURFER_DIR/bin/mri_info --cras ../mri/orig.LPI.nii | cut -f3 -d' '` MATRIX="1.0 0.0 0.0 $X_OFFSET 0.0 1.0 0.0 $Y_OFFSET 0.0 0.0 1.0 $Z_OFFSET 0.0 0.0 0.0 1.0" caret_command -surface-apply-transformation-matrix Human.$CASE.$HEM_FLAG.Midthickness.coor d Human.$CASE.$HEM_FLAG.topo Human.$CASE.$HEM_FLAG.Midthickness_orig.coord -matrix $MATRIX We have a standard import/preborder script for humans, but the monkey stuff tends to need tweaking: http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2009_10/PALS_B12.LR/preborder.sh login pub password download Most of the subroutines in that script won't apply, but the import steps might be helpful. On 07/30/2010 09:21 AM, Arslan, Ali wrote: > Hi, > I've done a macaque brain reconstruction in Freesurfer and I would > like to be able to view those surfaces concurrently with the > anatomical volume in Caret. I've followed the steps in one of the > tutorials but SURFACE & VOLUME view only contains the anatomical > volume, even though I can see the surface by itself in its model view. > > I was wondering whether I'm missing any basic steps before being able > to view both data together. Can I be doing anything wrong when I'm > importing either one of the data? > Any help would be appreciated, > Ali Arslan > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
