questions > dcm2niix-derived SliceTiming as input for fsl's slicetimer
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Dec 4, 2024  04:12 PM | Panos Fotiadis
dcm2niix-derived SliceTiming as input for fsl's slicetimer

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

Dec 4, 2024  05:12 PM | Chris Rorden
RE: dcm2niix-derived SliceTiming as input for fsl's slicetimer

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.

Dec 4, 2024  05:12 PM | Panos Fotiadis
RE: dcm2niix-derived SliceTiming as input for fsl's slicetimer

Ah perfect -- thanks so much, Chris!