I recently started using freesurfer for gray-white segmentation with great success. However, I have had one problem I cannot solve myself: I have been unable to create a ribbon file at the native resolution of my T1 scans (0.7 mm isotropic voxels), and I am puzzled by the result.
My strategy was as follows:
1. standard recon all (this works nicely) 2. resample aseg.mgz to match the slicing of rawavg.mgz 3. create new ribbon file using mris_volmask
The standard recon at 1x1x1 mm resolution produces a nice ribbon file: http://white.stanford.edu/~winawer/brain/2011/axial_ribbon_1mm.tiff
The hires recon after steps 2 and 3 above fails: http://white.stanford.edu/~winawer/brain/2011/axial_ribbon_hires.tiff
If anyone knows why this is, I would greatly appreciate the help.
For details, see below.
Many thanks,
Jon
The hires t1 I started with is here: http://white.stanford.edu/~winawer/brain/2011/t1.nii.gz
and the code I used for the initial recon and the creation of the new ribbon is here: # give the subject a name subj=homer
# recon all using hires t1 (0.7 mm isotropic voxels) recon-all -i ~/t1.nii.gz -all -subjid $subj -all
# define the working directory d=$SUBJECTS_DIR/$subj/mri
# back up original ribbon and aseg files mkdir $d/1mm; mv $d/*ribbon* $d/aseg.mgz -t $d/1mm
## Create Hi-Res Ribbon##################### # reslice the aseg file to the size and resolution of rawavg mri_convert $d/1mm/aseg.mgz -o $d/aseg.mgz --reslice_like $d/rawavg.mgz --resample_type nearest
# re-create surface at resolution of rawavg mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance $subj #####################################
# back up high-res files mkdir $d/hires; cp $d/*ribbon* $d/aseg.mgz $d/hires/
# Compare the two ribbon files. Original (1x1x1 mm) looks good: tkmedit $subj 1mm/aseg.mgz -segmentation 1mm/ribbon.mgz
# HiRes looks bad: tkmedit $subj hires/aseg.mgz -segmentation hires/ribbon.mgz
******************************* Jonathan Winawer Stanford University Department of Psychology Jordan Hall, Building 01-420 450 Serra Mall Stanford, CA 94305 Phone: 650-725-1255 winawer@stanford.edu http://www-psych.stanford.edu/~winawer/