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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share34
January 23, 2019 04:48PM
Hi,

I want to create a binary mask of the left rostralmiddlefrontal region from the Desikan-Killiany probabilistic atlas, TT_desai_dkpmaps+tlrc, so I ran the following command (to get a mask of all voxels > 25% in the probabilistic atlas):

3dcalc -a 'TT_desai_dkpmaps+tlrc[19]' -expr 'ispositive(a-0.25)' -prefix leftMFG

My first question is: Does this step yield a binarized mask (which is what I want)? Or do I have to run an additional command?

Next, I attempted to convert the above mask (left MFG) to MNI space. My resting functional data is normalized to MNI space and I could only find this specific atlas in Talaraich space. I found this old AFNI message board post (https://afni.nimh.nih.gov/afni/community/board/read.php?1,70173,80922#msg-80922) and tried the first couple of commands posted there.

3dWarp -tta2mni -prefix leftMFG_mni leftMFG+tlrc

3dWarp -matvec_out2in mni_fsl2tal.1D -prefix lMFG_mni2 lMFG25+tlrc

These steps both ran successfully. Can I use either option for converting the Desikan-Killiany ROI to MNI space? I am new to AFNI, and looked at a couple Message Board posts but I want to make sure I'm doing this correctly before running my seed-to-voxel resting fMRI analysis. Thanks!

~Stephanie
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Subject Author Posted

create ROI from TT_desai_dkpmaps atlas and convert to MNI space

share34 January 23, 2019 04:48PM

Re: create ROI from TT_desai_dkpmaps atlas and convert to MNI space

Daniel Glen January 24, 2019 05:37PM

Re: create ROI from TT_desai_dkpmaps atlas and convert to MNI space

share34 January 25, 2019 01:29PM

Re: create ROI from TT_desai_dkpmaps atlas and convert to MNI space

Daniel Glen January 25, 2019 01:51PM

Re: create ROI from TT_desai_dkpmaps atlas and convert to MNI space

share34 January 28, 2019 11:45AM