If you have it in some vtk format I guess matlab is probably the easiest using write_annotation.m
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 3:55 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 Hi,
The inquiry emerged due to an interest in using prebuilt R and/or Python visualization packages that only accept .annot as input. Is there some method of conversion to .annot given the aforementioned files I have?
Thanks again.
On Sat, Jun 12, 2021 at 2:08 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: If you already have it on the surface you don’t need it, do you?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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 <BFISCHL@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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 <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Evan
Is it a volumetric atlas or a surface one?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 11:33 AM To: freesurfer@nmr.mgh.harvard.edumailto: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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