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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RvK
February 07, 2020 09:36AM
Dear AFNI experts,

I am currenlty working on analyzing fMRI data using the 3dLME package. I stumbled upon 2 questions that I (as of now) could not find a satisfying answer to in the forum or through web search.

1. Is it advisable to use a group-level mask (created by running a second level analysis in SPM) for a 'whole-brain' analysis? It seems more intuitive to me to use a mask here that includes only the voxels that are actually present for all subjects, in contrast to no masking (which is the default for 3dLME).

2. How can I receive my alpha level for a cluster in the cluster report in AFNI (after manually putting in the voxel threshold from the 3dClustSim step in the gui)? Currently it says N/Csim in the Alpha column in the AFNI gui. I read that I may have to use 3drefit but I was unable to get it to work. Could you point me into the right direction? I am quite new to AFNI in general.

Please let me know if you need any more information.

Thanks in advance for your help!

Kind regards,
Rozemarijn
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Subject Author Posted

3dLME questions

RvK February 07, 2020 09:36AM

Re: 3dLME questions

gang February 07, 2020 01:31PM