If you already have it on the surface you don’t need it, do you?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
External Email - Use Caution
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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file
External Email - Use Caution
Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Evan
Is it a volumetric atlas or a surface one?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Evan Collins
Sent: Saturday, June 12, 2021 11:33 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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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