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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Ziad Saad
November 06, 2009 10:27PM
Hello Samir,

The program 3dAllineate allows you to specify masks or more generally weight volumes on the base volume (target) and a mask on the source (input) volume. I assume you are aligning the lesioned brain to the template. So try using the option -source_mask and provide it with a mask that excludes most of the lesion.

Of course, you'll need to create such a mask, but I suspect, you should get something decent with simple intensity thresholding.

If all that fails, upload the data and we'll take a look at this.

cheers,
ziad
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Subject Author Posted

Normalization Issue

Samir November 06, 2009 04:32PM

Re: Normalization Issue

Ziad Saad November 06, 2009 10:27PM