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 <[email protected]>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 <[email protected]
> > 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
>> [email protected]
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
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