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.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eTUXnQrBP5am9WANIUlhe4&e=
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eTUXnQrBP5am9WANIUlhe4&e=
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
