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