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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mrinmayi
April 11, 2018 06:47PM
Oh! Sorry about that!

This is a regular EPI dataset. I just chose this colour scheme in the overlay, because I find it easier to see if anatomical markers (e.g. ventricles) are lining up with the underlay. But this a regular EPI with continuous intensity. The anat I enter into align_epi_anat is also skull-stripped (and the skull-stripping is good). I'm doing volume registration, skull-stripping, etc in separate steps because align-epi-anat is crashing for a lot of my subjects when these steps are done together.

I'm just concerned about the voxels that fall outside the brain. These voxels are introduced in the alignment step because the epi before alignment looks okay. I'm also concerned about all the bleeding out in the normalised EPI. Is that normal?

Thank you,
Mrinmayi
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Subject Author Posted

Ghosting in alignment Attachments

mrinmayi April 09, 2018 12:15PM

Re: Ghosting in alignment

Daniel Glen April 10, 2018 12:21PM

Re: Ghosting in alignment

mrinmayi April 11, 2018 06:47PM

Re: Ghosting in alignment

Daniel Glen April 11, 2018 07:56PM