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/