AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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rsingh
September 10, 2012 11:03AM
The error I am getting is after running freesurfer on mprage T1 images. I am doing volumetrics study where I am using freesurfer to determine the measurements of cortical an dsubcortical regions. The subcortical masks as well as the white matter/gray matter outlines seems to be OK after the freesurfer run. I am using whole brain volume as a co-variate for statistical analysis, but due to errors in freesurfer skull stripping the brain masks are either including non-brain tissue or excluding some brain tissues. This will affect the whole brain volume calculation.
May you suggest how this skullstrip error may be avoided.
Is there a way to 3dskullstrip the data and then use the skullstripped mprage data to run freesurfer for obtaining cortical and subcortical segmentation?
Thank you!
Rashmi
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Subject Author Posted

FreeSurfer

rsingh September 07, 2012 03:19PM

Re: FreeSurfer

Peter Molfese September 07, 2012 11:02PM

Re: FreeSurfer

rsingh September 10, 2012 11:03AM

Re: FreeSurfer

Peter Molfese September 10, 2012 12:22PM

Re: FreeSurfer

rsingh September 11, 2012 10:35AM

Re: FreeSurfer

ziad September 11, 2012 05:07PM