If you already have it on the surface you don’t need it, do you?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Evan Collins
Sent: Saturday, June 12, 2021 1:12 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file

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Thanks for the info. I have the atlas surface (with vertex data) saved as a .vtk. Would the mris_sample_parc work with this input file type?

On Sat, Jun 12, 2021 at 1:01 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

I see. And what do you want to do with the annot and label files? Annots are surface parcellations only, so you would need to sample to a surface to get them. If you have a surface you can use mris_sample_parc to sample it onto the surface and create an annotation (I think Doug has something newer/better documented that will also do this, but I can’t remember what it is)

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Evan Collins
Sent: Saturday, June 12, 2021 12:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file

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Hi Bruce,

It is volumetric.

Thanks!

On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Hi Evan

Is it a volumetric atlas or a surface one?

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Evan Collins
Sent: Saturday, June 12, 2021 11:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Inquiry about creating .label files from .nii file

        External Email - Use Caution        

FreeSurfer,

I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files?

Thank you.

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