Hi Bruce,
Thanks so much for getting back to me on this! Yes, I have tried mri_cc with -f
and I am able to view part of the fornix along with the corpus callosum when I
call up the appropriate labels. However, I don't seem to be able to visualize
the two structures separately. Is it possible to separate the two? Thanks in
advance!
Regards,Maryam
On Thursday, August 6, 2015 1:22 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Maryam
try specifying -f on the mri_cc command line (as the first option)
cheers
Bruce
On Thu, 6
Aug 2015, Syeda Maryam wrote:
> Hi everyone,
>
> So I've been going through the list trying to see if someone has encountered
> the same problem as me with regards to segmentation of the fornix but have
> not found a solution as yet. I'm a grad student and still relatively new to
> freesurfer. My research group is using freesurfer to segment and visualize
> white matter tracts in data obtained from the ADNI database. We are
> primarily working with the subcortical segmentation in the aseg volume. My
> current issue is that I am unable to find the labels for the fornix in the
> aseg volume; they seem to only be located in the wm volume generated by
> freesurfer. When I try to run mri_cc on my aseg, the corpus callosum and
> fornix segmentation are output together and I'm unable to analyze them
> separately. I'd really like all the labels I require to be contained in a
> single volume rather than multiple ones as that will make my job a lot
> easier.
> Is there something I'm missing? Is there a way of extracting the fornix and
> corpus callosum, and indeed, all white matter tracts from the same volume?
> Any help will be highly appreciated!
>
> Thanks in advance,
> Maryam
>
>
>
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