Re: [Freesurfer] [FreeSurfer] WM Parcellation

First you'll have to decide on which wm parcellations will go into which lobe. When you have that, then you can use mri_binarize with the --replace option to change the index of a given segmentation to that of the lobe

On 01/27/2016 07:00 PM, VA Research wrote:

thank you for that,

but i'm confused on how to do the rest as well .

I now have the wmparc2 with unsegmented areas,

how can we create the lobar regions and use those to parcelate the WM into

lobar regions?

On Wed, Jan 27, 2016 at 2:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

You can regenerate a wmparc that does not have the unsegmented wm with
something like

cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
--volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o
mri/wmparc2.mgz

Then create your lobes from that


On 01/27/2016 05:47 PM, VA Research wrote:
> Hello FS experts,
>
> Does anyone have some form of step-by-step instructions on how to do
> this ?
>
> Thanks so much
>
> Joseph
> Brainiac . wrote:
> >/Hi All, />//>/I need to classify WM into different lobes
(temporal, parietal, />/frontal, occipital). I tried to do the
lobe mapping using />/parcellations from wmparc.mgz.
/>/http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
/>//>/My problem is the "unsegmented white matter" in wmparc.mgz.
My />/understanding is that these unsegmented areas are classified
so />/because they are beyond 5mm from any pre-classified cortex
area. />//>/My questions: />/(1) So in order to classify
"unsegmented WM" into lobes, do I need to />/take each voxel in
the unsegmented WM region and then assign it to the />/closest
cortex area to classify it into respective parcellations. Then
/>/re-group into lobes. Is this correct? /
> >//>/(2) Are there any tailor made function or any other easier
way to do />/this? Is there any easier way to segment WM into
lobes directly that I />/have missed? />//>/Thanks, />/Brain/
>
> You can do this in a couple of steps. First, you'll need to create a
> lobe annotation. You can do this in 3 ways:
>     1. mri_annotation2label --lobesStrict
>    2. mri_annotation2label --lobes
>    3. Custom: break up annotation and recombine:
>        a. mri_annotation to create separate label files
>        b. mri_mergelabels to create single label files for each
lobe label
>        c. mris_label2annot to create the lobe annotation
>
> Next, create the WM segmentation with mri_aparc2aseg, specifying
your
> new lobe annot and adding --labelwm. You can control the
distance  with
> --wmparc-dmax
>
> doug
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

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