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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bob cox
April 05, 2009 04:08PM
Steps 1 and 2 make sense, or you could use FreeSurfer in Step 1 (it's slow but accurate in segmentation).

I'm not sure what you want from Steps 3 and 4. You could use the mask from Step 2 to extract all the time series from CSF and/or WM via 3dmaskdump, and then compute a low dimensional approximation to these using the first few principal components from 1dsvd. Then you could use these as 'baseline' (or 'null hypothesis') regressors in 3dDeconvolve/3dREMLfit, or any other linear regression program of your choice.
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Subject Author Posted

white matter mask from EPI

Andrea Spadoni April 04, 2009 03:32PM

Re: white matter mask from EPI

bob cox April 05, 2009 08:47AM

Re: white matter mask from EPI

Andrea Spadoni April 05, 2009 09:51AM

Re: white matter mask from EPI

bob cox April 05, 2009 04:08PM