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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Lisa_Kr
November 11, 2015 08:24AM
Hello,

I'm a beginner and I have a problem with 3dmaskave and I hope someone can help me. I want to extract time series from a ROI applied to the subject's functional image. I have a ROI mask a 4D functional file. When I use the following command:

3dmaskave -mask /path/roi.nii.gz /path/bold.nii.gz

I get a 1D file containing only one number (one time point). But I would like to have averaged voxel intensity for every time point.
Here's the preprocessing steps I did prior to that:
- deobliquing, motion correction and brain extraction on the functional data (I checked and it is still 4D)
- transforming the ROI mask from the standard space into the functional space.

What could cause this problem?
I need the extracted time series to correlate it with the time series of all the other voxels in the brain.

Thanks!
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Subject Author Posted

3dmaskave problem

Lisa_Kr November 11, 2015 08:24AM

Re: 3dmaskave problem

Lisa_Kr November 11, 2015 10:08AM