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

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
Daniel Glen
March 06, 2015 12:03PM
You may set the options to how align_epi_anat.py sets the 3dSkullStrip options with "-skullstrip_opts" (possibly via afni_proc.py's "-align_opts_aea" option). Also consider skullstripping your data separately beforehand and skipping any skullstripping in afni_proc.py or align_epi_anat.py. Affine alignment is usually not very sensitive to precise skullstripping, so only extreme cases are critical here. For afni_proc.py, masking of the functional results to the skullstripped anatomical data is an option. See the MASKING note in afni_proc.py's help and the -mask_apply option.



Edited 1 time(s). Last edit at 03/06/2015 12:05PM by Daniel Glen.
Reply Quote
RSS
Subject Author Posted

align_epi_anat options to skullstrip

tsliu March 06, 2015 11:16AM

Re: align_epi_anat options to skullstrip

Daniel Glen March 06, 2015 12:03PM

Re: align_epi_anat options to skullstrip

tsliu March 08, 2015 04:27PM

Re: align_epi_anat options to skullstrip

Daniel Glen March 08, 2015 06:01PM

Re: align_epi_anat options to skullstrip

tsliu March 09, 2015 05:34PM

Re: align_epi_anat options to skullstrip

Daniel Glen March 09, 2015 06:47PM

Re: align_epi_anat options to skullstrip

tsliu March 10, 2015 09:34AM

Re: align_epi_anat options to skullstrip

Daniel Glen March 10, 2015 12:31PM

Re: align_epi_anat options to skullstrip

tsliu March 10, 2015 05:27PM

Re: align_epi_anat options to skullstrip

Daniel Glen March 10, 2015 06:19PM

Re: align_epi_anat options to skullstrip

tsliu March 11, 2015 02:57PM