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

History of AFNI updates  

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May 19, 2005 09:07AM
Too many questions at once, typed out in a format that is very hard to read (all run together). That is why the answers are delayed.

1) The mask dataset must be at the same resolution as the functional/EPI dataset to which you wish to apply it. If your functional dataset is already resampled to Talaraich coordinates at the same resolution as the mask (default resolution is 1 mm) then you do not need to resample the mask. Otherwise, you do need to resample the mask, probably using a command like

3dfractionize -template epi+tlrc -input mask+tlrc -prefix mask_resam -clip 0.4 -preserve

2) The Brodmann areas in the Talairach atlas supplied by U Texas are rather outline-y looking. This is what we have. It can be useful to look at the regions as you draw them in the "Render [new]" plugin. If you set up that plugin with the same overlay dataset that you are drawing into, turn on "ShowThru" and "See Overlay" and "See Xhairs" and "DynaDraw", then as you draw new values into the overlay dataset with the ROI plugin, you will also get a volume rendering update. (You cannot draw into the rendering window, though.)

3) The principal purpose of ROIs, to my mind, is to customize the analysis to the individual subjects. Therefore, I think that you should use the Talairach atlas regions only as a starting point for drawing your ROIs, and then you should manually edit the ROIs to match each subject's particular brain shape.

4) I know nothing about MRIcro.
Subject Author Posted

ROI MASK PROBLEMS.

Chunming Lu May 17, 2005 09:54AM

Re: ROI MASK PROBLEMS.

Robert Cox May 19, 2005 09:07AM

Re: ROI MASK PROBLEMS.

Chunming Lu May 19, 2005 09:33PM