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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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 CautionI 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 CautionCould 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 CautionHi 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 CautionI 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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:
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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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