Help with Preprocessing fMRI Data in SPM12

Software Support
1

Hey there, :smiling_face_with_three_hearts:

I am hitting a wall with slice timing correction in SPM12. I’ve been following different tutorials, but something just isn’t clicking.

For context, I’m working with data that started as DICOM files, converted them to NIfTI, got the functional images realigned, the anatomical image coregistered, and even tackled normalization to MNI space. Phew! But now I’m stuck on this slice timing business. My TR is 2 seconds and I have 36 slices. Every time I try to run the correction in SPM12, I get an error message that’s going way over my head.

Wondering if anyone else has been down this road before? Any advice on how to set up those slice timing parameters in SPM12 the right way would be a massive help.

Also, if you have any favorite resources or super clear guides on fMRI preprocessing in SPM12, I’d be eternally grateful!
I also check this resource: https://neurostars.org/t/how-to-run-preprocessed-fmriprep-datainspmqlik But I have not found any solution.

Thanks a bunch in advance for any help you can offer.

Respected community member :innocent:

2

To be able to help you may need to give us more info.

What did you actually try? What values did you use? SPM will require an acquisition time and a slice order or it can also work with the time at which each slice is acquired.
What error did you get? (copy paste the error message from the matlab command line rather than a screen capture)

Also note that even if I agree it is super important to do some preprocessing yourself to wrap your head around the different steps and what they do, I would suggest trying to ultimately aim to use preprocessing pipelines (like fmriprep - or bidspm if you really have to stick to SPM) so you do not have to reinvent the wheel.