Dear all, 

I'm writing to ask a question about my data. I have two acquisition in resting state fMRI for each subject: one pre-treatment and one post-treatment.

I have reoriented the T1 and rs-fMRI images for each subject's condition. Then in CONN setup I set the number of subjects and the number of session (2) together with the TR. After that, I selected the T1s and rs-fMRIs and setup the two conditions (pre and post).

After running the first preprocessing step I obtained these images that I attach here.

What's wrong with all the images?

Any help would be very appreciated.

Best,

Beatrice

Dear Beatrice

The data does not appear to be fully or correctly preprocessed (e.g. the functional and anatomical data does not appear to be coregistered or in MNI space). If you have not done so yet, go to the Setup tab and click on 'run preprocessing' and select and run the default preprocessing pipeline in there. That should put your data in MNI-space and also create a number of 1st-level covariates (such as realignment and scrubbing variables) that will allow you to properly denoise your data.

Hope this helps

Alfonso

Originally posted by Beatrice Bravi:

Dear all, 

I'm writing to ask a question about my data. I have two acquisition in resting state fMRI for each subject: one pre-treatment and one post-treatment.

I have reoriented the T1 and rs-fMRI images for each subject's condition. Then in CONN setup I set the number of subjects and the number of session (2) together with the TR. After that, I selected the T1s and rs-fMRIs and setup the two conditions (pre and post).

After running the first preprocessing step I obtained these images that I attach here.

What's wrong with all the images?

Any help would be very appreciated.

Best,

 

Beatrice

Hi, all.

I suspect the problem is similar to one that I am experiencing with CONN/SPM12, in which some participants longitudinal scan data is not unwarping and realigning properly during the early preprocessing stage.  

I haven't tested it yet, but I suspect for some participant imaging data that the 0,0,0 centering function in CONN is impeding proper registration over timepoints?  

I thought initially the problem might be where the origin is located when the images come off our scanner, so I reoriented the origin to the AC along the AC-PC line and then coregistered (estimate only) the corrected origin from the baseline scan to the subsequent scans for a participant.  Everything looked great and in reasonable alignment prior to starting CONN/SPM12 preprocessing, but I continue to receive clearly problematic results for some participants.  The fact that it doesn't screw up for all participants has me stumped.  

See attached as a gross example of the problem with realignment over scans/time.

Any thoughts or possible solutions?

Warm regards,

Jeff