Should I make up my own LUT for the new ROIs that specifies some colour and
label number?
On Wed, Apr 9, 2014 at 10:00 AM, Corinna Bauer <corinna...@gmail.com> wrote:
> It looks like the FreeSurferColorLUT.txt does not contain the label number
> for the newly created labels (divided from the desikan atlas).
>
>
> On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl
> <fis...@nmr.mgh.harvard.edu>wrote:
>
>> $FREESURFER_HOME/FreeSurferColorLUT.txt
>>
>> cheers
>> Bruce
>> On Wed, 9 Apr 2014, 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>
>> > 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> 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
>> > gr...@nmr.mgh.harvard.edu
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