Ok I did and inserted only this:

#No. Label Name:                            R   G   B   A

1   Left-Cerebral-Exterior                  70  130 180 0

since I binarized the lesion masks and when creating the label I assigned value 1 (with the option --id 1). Is it correct?

Thanks,

Vale

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Friday, February 15, 2019 1:56:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

 

you have to create your own. Use FreeSurferColorsLUT.txt as your template

On 2/15/19 1:08 PM, Barletta, Valeria wrote:

Ok thank you, it works but there is a problem... The command mris_label2annot requires a ColorTable file.

As I tried to use FreeSurferColorLUT.txt    I got a list of all regions I did not need.

What kind a ColorTable file shall I provide to create an annotation file for cortical lesions only?

Thank you,

Vale

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Thursday, February 14, 2019 3:37:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

 

You can make separate labels (mri_cor2label with --surf option), then
use mris_label2annot

On 2/14/19 3:32 PM, Barletta, Valeria wrote:
>
> Yes sure,
> I need to extract values from discrete cortical lesions, but I have
> masks of all lesions together projected to the cortical surface.
>
> I have a script that can provide me values for every single lesion
> separately, but this script works on annotation files.
>
> Is it possible to create an annotation file for the lesion masks? They
> are in   .mgh  format
>
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <DGREVE@mgh.harvard.edu>
> *Sent:* Thursday, February 14, 2019 3:28:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface cortical lesions mask -->
> annotation file ???
> not sure what you mean, can you elaborate?
>
> On 2/14/19 2:05 PM, Barletta, Valeria wrote:
> >
> > Dear Freesurfers,
> >
> > I need to extract annotation files from my cortical lesion masks
> > projected to the surface.
> >
> > Do you know whether this is possible?
> >
> > Thank you,
> >
> > Valeria
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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