Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?
Hi Andy,
I found out that mris_convert has ‘-f’ flag to specify functional file. The
syntax is
mris_convert -f 395091.R.func.gii rh.shen.atlas.mgh
You also need to specify a valid surface file as the 3rd argument
urfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Andy Kim
Sent: Monday, January 9, 2023 8:25 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?
External Email - Use Caution
Hi Yujing,
rh.shen.atlas.1.label is just an output name. It can b
ng, Yujing
Sent: Tuesday, January 10, 2023 12:17 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?
Hi Andy,
I would like to reproduce ‘mri_vol2label --c 395091.R.func.gii --id 1 --l
rh.shen.atlas.1.label --surf fsaverage rh’. Woul
nt: Sunday, January 8, 2023 1:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?
External Email - Use Caution
Hi Yujing,
Yes they are the files I downloaded.
I tried:
mris_convert 395091.R.func.gii rh.shen.atlas.mgh
and I go
...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Friday, January 6, 2023 11:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?
Hi Andy,
Thanks for the information.
The error message that you are getting is actually from GIFTI library. I’m
urfer support list
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?
External Email - Use Caution
Hi Yujing,
I got the surface-based shen 268 atlas GIFTI file from Neurovault: MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com"
.edu
on behalf of Huang, Yujing
Sent: Thursday, January 5, 2023 10:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation?
Hi Andy,
Based on my understanding from GIFTI specification, your .gii are functional
files. I’m not sure
5, 2023 3:05 AM
To: freesurfer
Subject: [Freesurfer] How to convert surface-based atlas to annotation?
External Email - Use Caution
Dear FreeSurfer Developers,
To analyze functional connectivity, I first got Shen 268 surface-based atlas
from Neurovault. Now I want to extract average t
External Email - Use Caution
Dear FreeSurfer Developers,
To analyze functional connectivity, I first got Shen 268 surface-based atlas
from Neurovault. Now I want to extract average time series data from my
subjects based on the atlas but I have no idea how to make annotation.
