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. Please note that e-mail communication is not encrypted >> by default. You have the right to request further emails be encrypted >> by notifying the sender. Your continued use of e-mail constitutes >> your acknowledgment of these confidentiality and security >> limitations. If you are not the intended recipient, be advised that >> any unauthorized use, disclosure, copying, distribution, or the >> taking of any action in reliance on the contents of this information is >> strictly prohibited. >> If you have received this e-mail in error, please immediately notify >> the sender via telephone or return e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har >> vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGl >> LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& >> m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5 >> eTUXnQrBP5am9WANIUlhe4&e= > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLD > GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=j > jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eTUX > nQrBP5am9WANIUlhe4&e= > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD > GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7BDZ5Vmt5nwPIL5NPyilKyo&e= > > > ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
