AFNI Message Board

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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.
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



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