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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Daniel Glen
August 15, 2007 05:41PM
I'm not sure where the problem is, but you might look at the output of 3dclust with the -prefix option to save a clustered dataset. Compare and overlay this dataset with the 3dmerge output. Your 3dmerge command has a 0 volume, but I assume this is just a typo here.

The default orientation may be set via the AFNI_ORIENT variable in a .afnirc file or set in the environment. The default display coordinates in the AFNI GUI are set to RAI/DICOM in the top left corner of the GUI. Right clicking there will allow you to choose LPI/SPM as an alternative. The -orient option you specified forces the output of 3dclust to give results in LPI order.

Your 3dmerge command sets the values of each cluster in the order of the largest to smallest clusters. You can use a 3dcalc command to separate the clusters into separate datasets if you like.

You can post the output of 3dinfo on the decon_1_results+orig dataset to see if we can get any more clues from that.
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Subject Author Posted

ROI analysis

Victor August 15, 2007 03:33PM

Re: ROI analysis

Daniel Glen August 15, 2007 05:41PM

Re: ROI analysis

Victor August 16, 2007 12:50PM

Re: ROI analysis

Daniel Glen August 16, 2007 02:50PM