Hi Donna, After I sent my first email, I was able to see the anatomical volume overlaid on the surface, just like visualizing a functional volume, by using the 'Map volume(s) to surfaces' tool. The results were not great because the surface and the volume didn't overlap at all. (please see the picture here) http://img686.imageshack.us/img686/7214/screenshot20100730at132.png
So I took your suggestion and tried that transformation code you pasted. I couldn't complete it because there was a bus error, which is a hard to circumvent. echo $MATRIX 1.0 0.0 0.0 -0.43635 0.0 1.0 0.0 10.7291 0.0 0.0 1.0 15.8675 0.0 0.0 0.0 1.0 caret_command -surface-apply-transformation-matrix lh.orig lh.orig.topo lh.orig.trans -matrix $MATRIX (I couldn't find in the documentation whether 'lh.orig.topo' part I wrote is an input or an output but I included it as a placeholder, there's no such file) Can you suggest another tool to apply that transformation? Or do you have any idea what went wrong? Couple of other questions: 1) Can I do this transformation manually, by nudging the surface or the volume or defining AC PC landmarks? 2) I can't see the loaded volumes in the 'Map volume(s) to surfaces' tool's volume selection dialogue, so I have to read it from the disk again. This is the same if I use a spec file or if I load a surface and a volume by hand without a spec. 3) Even though surface and the volume are in different orientations, shouldn't I be able to see them (even though misaligned) in the Surface $ volume view? Best, Ali --------------------- 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 Fri, Jul 30, 2010 at 10:21 AM, Arslan, Ali <[email protected]> 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
