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

History of AFNI updates  

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March 25, 2020 02:35PM
Well I looked thru the proc generated from afni_proc.py and this looks like the one that does it:

# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, mprage_ns+orig)
align_epi_anat.py -anat2epi -anat mprage+orig \
-save_skullstrip -suffix _al_junk \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-cost lpc+ZZ \
-volreg off -tshift off

There is no separate deskulling command. This is the first one (that I see) in the proc that does something about deskulling.

MIke
Subject Author Posted

Problem with deskulling 7T scan

mikek March 24, 2020 02:48PM

Re: Problem with deskulling 7T scan

ptaylor March 24, 2020 03:19PM

Re: Problem with deskulling 7T scan

mikek March 25, 2020 02:35PM

Re: Problem with deskulling 7T scan

ptaylor March 25, 2020 02:53PM

Re: Problem with deskulling 7T scan

mikek March 25, 2020 03:16PM

Re: Problem with deskulling 7T scan

ptaylor March 25, 2020 04:36PM

Re: Problem with deskulling 7T scan

mikek March 26, 2020 09:00AM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 09:35AM

Re: Problem with deskulling 7T scan

mikek March 26, 2020 09:49AM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 10:25AM

Re: Problem with deskulling 7T scan

mikek March 26, 2020 01:28PM

Re: Problem with deskulling 7T scan Attachments

mikek March 26, 2020 05:35PM

Re: Problem with deskulling 7T scan

mikek March 27, 2020 08:21AM

Re: Problem with deskulling 7T scan

ptaylor March 27, 2020 09:21AM

Re: Problem with deskulling 7T scan

Colm Connolly March 26, 2020 09:11AM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 09:33AM

Re: Problem with deskulling 7T scan

Colm Connolly March 26, 2020 04:53PM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 05:17PM