yes, do it on fsaaverage and it will more-or-less be in the common
coordinate space.
cheers
Bruce
On Mon, 10 Dec 2018, Song, Da-Yea wrote:
External Email - Use Caution
Hi Bruce,
I've taken a look at the mri_annotation2label command and it seems like
it requires a specific subject to run this command. We were looking to
pull out the ROI from the Desikan atlas (rather than from a particular
participant). Is there a way to do that?
Thank you so much in advance,
Da-Yea
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, December 07, 2018 3:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Extracting ROI from atlases
the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec
2018, Song, Da-Yea wrote:
External Email - Use Caution
I really appreciate the quick reply back Bruce!
I tried the following: mri_binaraize --i lh.aparc.annot --match 1023
--o ctx-lh-posteriorcingulate and got the error message saying
mri_read(): couldn't determine type of file
/usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot
Any suggestions?
Thank you,
Da-yea
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Friday, December 07, 2018 3:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Extracting ROI from atlases
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018,
Song, Da-Yea wrote:
External Email - Use Caution
Could you please direct me on where I could find the fsaverage annot file for
the Desikan atlas?
Thank you,
Da-Yea
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Friday, December 07, 2018 3:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers
Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use Caution
Hi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the
Desikan atlas (rather than from a particular subject). Do you have any
suggestions on what file I could use?
Thank you,
Da-Yea
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Friday, December 07, 2018 3:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the
fsaverage subject you can use, and of course we automatically
parcellate each subject that is run through recon-all. The gcs is
contains a lot of information that isn't easily displayed as an ROI,
so you can't really just extract one from it
cheers
Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use Caution
I tried this on the
?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error
message that mri_read could not determine the type of file. Do I need to
convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best,
Da-yea
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
N.,Ph.D.
Sent: Thursday, December 06, 2018 11:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use
mri_binarize --i aparc+aseg.mgz --match 1028 --o
ctx-lh-superiorfrontal.nii.gz See
$FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to
use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in
nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
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