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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Lukas Pezawas
January 07, 2003 07:27PM
Hi AFNI experts!

I tried to extract brains from MPRAGE images within AFNI using 3dIntracranial and I do not get good results. Therefore, I had to change manually the defaults of 3dIntracranial, which improved the results a bit. However, a rather time consuming manual editing procedure with the drawing plug in was necessary and I got a little tired of it.
Therefore, I tried brain extraction with Freesurfer and BET and results looked amazingly good. However, the orientation changed, when I tried to convert these images back to AFNI BRIK format and it seems that I lost on the way the information of the original position and orientation of the head, which I need to do a good nudging with 3dAnatnudge.

It would be very helpful, if anybody could tell me, how I could re-apply the spacial information of the original head BRIK file to the brain extracted BRIK file derived from ANALYZE (BET) or COR (Freesurfer) files.

Thanks,


Lukas
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Subject Author Posted

brain extraction

Lukas Pezawas January 07, 2003 07:27PM

Re: brain extraction

Tim Souza January 08, 2003 01:35PM

Thanks

Lukas Pezawas January 08, 2003 05:13PM

Re: brain extraction

Matthew Belmonte May 12, 2003 12:07PM