Hi Jon,

the surfaces are represented in the continuum, so should be able to help with the blockyness, but their coordinates are associated with a particular volume, and need to be remapped to do what you want.

cheers Bruce On Thu, 14 Apr 2011, Jonathan Winawer wrote:

Thanks. I did also map the ribbon.mgz file directly. This works without error and produces a pretty good segmentation. But it is a little blocky because of the upsampling. I was hoping that mris_volmask would give a slightly better result because it would take advantage of the fact that (as far as I can tell) the surface representations are not fixed to the voxel grid - the surfaces appear to be represented at higher resolution. (I infer this just by looking at images like this: http://white.stanford.edu/~winawer/brain/ surf.png)

But maybe this will not provide any benefit beyond your suggestion of just remapping the ribbon.mgz directly. In any case I will try mris_volmask after mri_surf2surf, as you suggest, and see if this works, and then compare the results to directly remapping the ribbon file.

Thanks for the suggestions

Jon

On Apr 14, 2011, at 6:20 AM, Bruce Fischl wrote:

...

Hi Jon

why not just map the ribbon.mgz directly? If you want to rerun mris_volmask you will need to map the surfaces to the highres dataset. I think you could do this with mri_surf2surf, although you may need to use tkregister2 -regheader to create a register.dat file for you. Doug would know.

cheers Bruce

On Wed, 13 Apr 2011, Jonathan A Winawer wrote:

...

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

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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/

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