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 >>> >>> -------------------------------------------------------------------- >>> - >>> --- >>> Disclaimer: >>> >>> >>> The materials in this e-mail are private and may contain Protected >>> Information. 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