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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Peter Molfese
September 08, 2021 08:54AM
My recommendation is to reprocessing using Subject_SurfVol.nii as your "anat" dataset in afni_proc.py with the -anat_has_skull set to "no". Then make sure that you have things aligning to the anatomical via -volreg_align_e2a. I've found this is generally the safest and also benefits from all of the AFNI automated QC images.

As an alternative, you can use @SUMA_AlignToExperiment and specify your follower datasets to include your aparc and aseg datasets.

Also if you're not already doing so, we generally recommend using the -NIFTI flag in your @SUMA_Make_Spec_FS commands.
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Subject Author Posted

Create a mask from a huge cluster Attachments

Mpark September 06, 2021 05:06AM

Re: Create a mask from a huge cluster

Peter Molfese September 06, 2021 08:31PM

Re: Create a mask from a huge cluster

Peter Molfese September 06, 2021 11:20PM

Re: Create a mask from a huge cluster

Daniel Glen September 07, 2021 10:12AM

Re: Create a mask from a huge cluster Attachments

Mpark September 08, 2021 02:09AM

Re: Create a mask from a huge cluster

Peter Molfese September 08, 2021 08:54AM

Re: Create a mask from a huge cluster

Daniel Glen September 09, 2021 11:54AM