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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heffjos
February 21, 2020 11:15AM
In a previous post, the recommended steps to warp brains with lesions were this:

  1. Draw the exclusion mask over the subject's image dataset.
  2. Register the template to the subject's dataset, and then apply the inverse of the warp transformation to get the subject's exclusion mask into template space. We need to do this because '-emask' option applies to the base dataset.
  3. Manually assemble correct processing stream using the exclusion mask. Use @SSwarper or auto_warp.py as a reference for the processing stream.

For 2, what should be used for registration? Should I use align_epi_anat.py?

For 3, I have not looked into it too much right now, but I plan on using @SSwarper as a reference to create the warping stream. I am assuming I will use the '-emask' option for all calls to 3dAllineate and 3dQwarp.
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Warping T1s with lesions to a base template space

heffjos February 21, 2020 11:15AM