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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dmoracze
December 15, 2014 12:06PM
Hello,

I would like to use Freesurfer a surface / segmentation for processing in AFNI. I have run @SUMA_Make_Spec_FS.
I first want to use aseg.nii to create masks to regress out wm and ventricle signal. However, aseg.nii does not align with the T1 or epi AFNI datasets.

I have tried @SUMA_AlignToExperime -exp_anat <T1+orig created with to3d> -surf_anat <aseg.nii> -prefix <prefix> -align_centers -final NN
Should -surf_anat be aseg.nii or surfvol? I have tried both but it doesn't seem to matter.

I have also tried 3dAllineate, and align_pi_anat.py and it doesn't seem to be making a difference.


Thanks!
Dustin



Edited 1 time(s). Last edit at 12/15/2014 10:39PM by dmoracze.
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Subject Author Posted

@SUMA_Make_Spec_FS alignment

dmoracze December 15, 2014 12:06PM

Re: @SUMA_Make_Spec_FS alignment

dmoracze December 15, 2014 12:30PM

Re: @SUMA_Make_Spec_FS alignment

ziad December 16, 2014 09:24AM

Re: @SUMA_Make_Spec_FS alignment

dmoracze December 29, 2014 12:56PM