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