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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Daniel Glen
December 31, 2018 12:27PM
You can turn off skullstripping for anat and epi datasets in align_epi_anat.py. The weighting for the epi data is applied in any case, and there is no option to turn it off, but that's not what you are interested in here, I think. The mask for the anatomical dataset is usually computed with 3dSkullstrip. If you turn that off, then all voxels are used. You can turn the skullstripping off with "-dset1_strip None" or "-anat_has_skull no". If you want to compute alignment for a masked dataset and apply the transformation to another dataset, you can use the "-child_anat" or "-child_epi" options.
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Subject Author Posted

add brainmask in align_epi_anat

ruyuanzhang December 30, 2018 11:39PM

Re: add brainmask in align_epi_anat

Daniel Glen December 31, 2018 12:27PM

Re: add brainmask in align_epi_anat

ruyuanzhang January 02, 2019 02:52PM

Re: add brainmask in align_epi_anat

Daniel Glen January 02, 2019 03:47PM

Re: add brainmask in align_epi_anat

ruyuanzhang January 10, 2019 05:24PM

Re: add brainmask in align_epi_anat

Daniel Glen January 10, 2019 05:29PM

Re: add brainmask in align_epi_anat

ruyuanzhang January 11, 2019 12:58AM