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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ptaylor
April 04, 2019 10:36AM
Hi, Sungshin-

I would give @SSwarper a try on your original dataset.

It should produce a skullstripped+unifized version in the original space; a nonlinear transformation to standard space (e.g., MNI), and a representation of the brain warped to standard space. It can be a bit slow-- a couple hours on a laptop-- but if you can run on a multicore machine, you can specify the number fo threads to use (it is parallelized using OpenMP) by setting the environment variable OMP_NUM_THREADS.

Assuming you have an uptodate version of AFNI ("afni -ver" to check, "@update.afni.binaries -d" to update), you can run something like: 
@SSwarper          \
        -input  DSET_T1_ORIG        \
        -base   MNI152_2009_template_SSW.nii.gz        \
        -subid  SUBJ_NAME        \
       -odir   .
... and please check the help file for more info (e.g., file names, automatic QC images made, etc.).

--pt
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Skull stripping and other EPI & MPRAGE registration issues Attachments

sungshinkim April 04, 2019 03:40AM

Re: Skull stripping and other EPI & MPRAGE registration issues

ptaylor April 04, 2019 10:36AM