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
February 06, 2018 09:40AM
The direct way to do this would be to
1) extract the 503 time series from the ROI using a command like 
3dmaskdump -noijk -mask ROImask.nii -o ROIdump.1D timeseries.nii
2) transpose the output file so that each column is a voxel timeseries, rather than each row 
1dtranspose ROIdump.1D > ROIts.1D
3) Produce a 503 sub-brick dataset of the correlation of each column with all voxels: 
3dTcorr1D -pearson -prefix ROIcorr.nii -mask Brainmask.nii timeseries.nii ROIts.1D
The i-th volume in the output dataset ROIcorr.nii will have the correlations of the i-th column in ROIts.1D with all the voxel timeseries from ROIts.1D. If you now want to extract all those to a text file, you can do that with 3dmaskdump. Note that this would be a pretty big file: 503 correlations times (say) 100,000 brain voxels = 50.3 million numbers in text form.
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Subject Author Posted

Correlation matrix

carolege February 06, 2018 08:17AM

Re: Correlation matrix

rick reynolds February 06, 2018 09:07AM

Re: Correlation matrix

ptaylor February 06, 2018 09:27AM

Re: Correlation matrix

carolege February 06, 2018 09:36AM

Re: Correlation matrix

Bob Cox February 06, 2018 09:44AM

Re: Correlation matrix

carolege February 06, 2018 09:47AM

Re: Correlation matrix

Bob Cox February 06, 2018 09:40AM