Afni Statistical Output Shows No Activation

Dear All,

We are working on a dataset in which our task is triggered by a series of auditory stimuli. We switched to a different fMRI scanner at some point in the study and with regard to the data collected on the new scanner, we are observing no brain activation for the study participants. We have checked if the stimulus files are being generated correctly, and if the initial TRs are being removed from the dataset appropriately before it goes through the, to check if inappropriate time shifts cause a kind of asynchrony between brain activity and the given stimuli. But this was not the issue either. One issue we were suspicious about was that with the new scanner the image is being recorded in a mosaic format, and we were wondering if the dcm2nii_afni is still a good command for the conversion of our DICOM files, or if there are any other or a more updated version of this command that can help with mosaic images.

We highly appreciate any ideas or recommendations in this regard.


Hi Sanaz,

Try running InstaCorr on it (without the first few volumes), using a seed where you would expect responses to auditory stimuli. Search around a little, spatially. It should be easy to see if there is something in the data.

Since you switched scanners, maybe it is possible the volumes are now out of order. You can check that with Dimon, using a command like:

Dimon -infile_pattern "run1/*.dcm" -dicom_org -save_details DET -gert_create_dataset

If you have questions about that, please send me email with the DET text files.

  • rick

Dr. Reynolds,
Thank you very much for your response and guidance.