Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

you'll need to figure it out from the volume itself by loading the seg with both -seg and -aux. When you find the label you want, click on it and the aux value in the control window will tell you what the id is

doug

On 04/09/2014 09:41 AM, Corinna Bauer wrote:

In the mri_extract_label, there is a label number. Where would I find this for the new labels?

i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035 ${subj_dir}/hardi_labels/ctx-rh-insula.nii

On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

yep, exactly


On 4/8/14 6:00 PM, Corinna Bauer wrote:

...

Hi Doug,
After I have the labels then in each subject's T1 space, I will
need to then put them into diffusion and resting state space.

I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using bbregister,
tkregister2, mri_vol2vol (using the inverse registration from
bbregister to put the T1 into diffusion space), mri_extract_label
(extract labels from aparc+aseg.mgz), and then mri_label2vol
(register each of the extracted labels into diffusion space).
Would a similar approach work for the new labels?

Corinna


On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:


    Exactly what you have described won't work very well because
    it would be
    in the volume. I would divide up the parcellations in
    fsaverage space
    like you've done, then map the parcellation to each subject using
    mri_surf2surf (--sval-annot, see example 6)

    doug

    On 04/08/2014 04:54 PM, Corinna Bauer wrote:
    > Hello all,
    >
    > I am planning to use mris_divide_parcellation to split the
    Desikan
    > atlas into smaller ROIs, but will need the new ROIs to be
    consistent
    > between subjects.
    >
    > Can I achieve this if I register each subject to fsaverage
    space and
    > then apply the inverse transform to the divided
    parcellations (which
    > are currently done on the fsaverage brain)?
    >
    > If so, for extracting each label, what would be used for
    the label
    > number?
    > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
    > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
    >
    >
    > Thanks
    >
    > Corinna
    >
    >
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