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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Mpark
September 08, 2021 02:09AM
Thanks for the great suggestions, Peter and Daniel!

I'm doing one by one you've suggested.
As for the suggestion by Peter, I've noticed I have subject's Freesurfer atlas after making retinotopic map. So I successfully did the whole procedure and created the conjunction of freesurfer atlas and my four chunks mask.
But I noticed that the T1.nii in SUMA generated after doing Freesurfer things is not aligned with my T1 file after preprocessing procedure (skull strip, deoblique etc.).
Can I align the SUMA files (e.g. apar.aseg.nii) to my epi or skull-stripped T1 data?

Currently, I'm looking at 3dmask_tool, and I've got a mask of the two occipital clusters ('A mask after 3dmask_tool' in the attached) among the four clusters ('A huge cluster' in the attached).
But what if I want to create a mask the removed, temporal side of two cluster which is the bilateral MT+ ('These are my interest' in the attached)?
If this is possible, it would be the best way for my situation!!

Plus, what's the meaning of level for '-dilate_inputs' in 3dmask_tool?

Thank you all so much! Your advice always helpful!



Edited 1 time(s). Last edit at 09/08/2021 02:13AM by Mpark.
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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