For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I follow
the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer <corinna...@gmail.com> wrote:
> Perfect. Thanks!
>
>
> On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> 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
>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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
>> >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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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>> >> --
>> >> Douglas N. Greve, Ph.D.
>> >> MGH-NMR Center
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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