This is kind of what happens during generate_depth in my preborder.sh script:
http://pub:[email protected]/pub/donna/FREESURFER/SCRIPTS/2010_12/PALS_B12.LR/preborder.sh login pub password download generate_depth() { CASE=$1 HEMISPHERE=$2 HEM_FLAG=`echo $HEMISPHERE | cut -c1 | tr '[:lower:]' '[:upper:]'` SPEC=Human.$CASE.$HEM_FLAG.73730.spec echo Generating depth for $CASE $HEMISPHERE # need to create volume to generate segmentation from fiducial caret_command -volume-create 176 208 176 Human.$CASE.$HEM_FLAG.segmentation.nii caret_command -volume-set-origin Human.$CASE.$HEM_FLAG.segmentation.nii Human.$CASE.$HEM_F LAG.segmentation.nii -88.0 -123.0 -75.0 caret_command -volume-set-spacing Human.$CASE.$HEM_FLAG.segmentation.nii Human.$CASE.$HEM_ FLAG.segmentation.nii 1.0 1.0 1.0 # generate segmentation from fiducial FIDUCIAL=deformed_Human."$CASE.$HEM_FLAG".Midthickness_711-2B.coord TOPO=Human.$CASE.$HEM_FLAG.CLOSED.73730.topo caret_command -surface-to-segmentation-volume $FIDUCIAL $TOPO Human.$CASE.$HEM_FLAG.segmen tation.nii # generate hull volume, surface, depth (shape), and geography paint files caret_command -surface-identify-sulci $SPEC $HEMISPHERE Human.$CASE.$HEM_FLAG.segmentation .nii $TOPO $FIDUCIAL $FIDUCIAL NIFTI_GZIP } On 01/24/2011 06:48 PM, Tristan Chaplin wrote: > Hi everyone, > > I've made a few models from histological slices and I was wondering if > there is any way of calculating sulcal depth without an MRI volume or > atlas. There aren't any MRIs for my animals and there aren't any > atlases for this species. > > I understand the I need a "cerebral hull", which is usually generated > by dilating and eroding the mid thickness of the MRI volume. I tried > to simulate this by slightly inflating the fiducial surface and saving > it as a vtk file and using it as a cerebral hull. It works ok, but I > was wondering if anyone knows a better way. > > Thanks, > Tristan > ------------------------------------------------------------------------ > > _______________________________________________ > 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
