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
May 03, 2017 03:33PM
Hi Jared-

Nice to know someone reads the blog!

I tend to use the -T2pial option with Freesurfer 6, which seems to do a pretty decent job handling dura for me. This has been true whether I'm using a standard T1 MRPAGE or a MEMPRAGE. You could collect just one T1 (MEMPRAGE), but I would stay vigilant about making sure that your T1 is good quality and not contaminated with motion. Not having a T2 usually isn't as painful as not having a good T1. I tend to lean towards the "more data is better" mentality.

My afni_proc.py scripts all use -giant_move, and align the EPI to the anatomical. I also use auto_warp.py (-tlrc_NL_warp) to help bring group level ROIs back to subject space with a bit more precision.

-PM
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Subject Author Posted

Scanning on two consecutive days: which anatomical to use?

Jared Saletin May 01, 2017 04:48PM

Re: Scanning on two consecutive days: which anatomical to use?

Peter Molfese May 02, 2017 04:23PM

Re: Scanning on two consecutive days: which anatomical to use?

Jared Saletin May 03, 2017 12:18PM

Re: Scanning on two consecutive days: which anatomical to use?

Peter Molfese May 03, 2017 03:33PM

Re: Scanning on two consecutive days: which anatomical to use?

Jared Saletin May 03, 2017 04:04PM

Re: Scanning on two consecutive days: which anatomical to use?

Peter Molfese May 03, 2017 04:50PM