Hello,
I would like to apply slice timing correction on a resting-state fMRI scan using FSL's slicetimer. I have already used dcm2niix (version: v1.0.20190902) to derive the json sidecar of the scan which has provided me with the 'SliceTiming' variable (which if I'm not mistaken should be in seconds).
I just wanted to verify: Would it be ok to create a text file containing the values under 'SliceTiming' and use that as the input to slicetimer's --tcustom flag? I was curious since I believe I read in the command's description that --tcustom is supposed to contain values in "fractions of TR." Or should I just derive new values = each value under 'SliceTiming' / TR and use these as input?
Thank you in advance, and apologies if I should direct this to the FSL forum instead!
Cheers,
Panos
This is correct. You will want to divide each element of the SliceTiming array by the RepetitionTime. ChatGPT could help you create a simple Python script to convert a BIDS JSON sidecar into a fsl slicetimer format ingle-column text file and then run slicetimer for you. This is a bit out of scope for dcm2niix, so you can also ask the FSL jiscmail group for FSL specific questions.
Ah perfect -- thanks so much, Chris!