I have some questions regarding the output of the fMRIPrep pipeline. I uploaded two images from the output-html here: https://kth.box.com/s/tclu502bicoc5tgtl7yweeo9hj3bt4r1
(the images need to be downloaded and then opened with Google Chrome). My questions are:
sub-01: This is the “ROIs in BOLD space” - output image from the html for one subject. I solely chose this image to point out the visible intensity differences from slice timing artefacts. I wonder now if this is because the shown image is the previously calculated reference image of the BOLD image? Or did the slice timing correction not work properly? Do you know where this comes from and if it is acceptable? From my knowledge, the slice timing correction works without errors (all inputs and outputs in the report file seem to be ok).
sub-02: This is a gif of the BOLD image before / after distortion correction. There is an artefact created at the prefrontal cortex and I don’t know if this is acceptable. In all my subjects, the white and grey matter are better aligned with the boundaries calculated before (blue line), but some tend to have this artefact. Does anybody have an opinion about it?
My inputs in the pipeline were:
fmriprep-docker /BIDS_data /output_dir participant -w /work_dir
–template MNI152NLin2009cAsym --output-space template --use-aroma
and I provided slice timing times and a fieldmap image. I calculated the times for STC based on the information I was given as:
“SliceTiming”: [0.0, 1.0733333333333335, 0.04666666666666667, 1.12, … , 2.006666666666667, 0.98, 2.0533333333333337, 1.0266666666666668]
(RT = 2.1s and number of slices is 45 with interleaved and ascending order.)
I calculated the fieldmap based on the FUGUE website from FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide). The fieldmaps looked okay in my opinion, with a median of ~10-50Hz up to 150-200Hz in areas of the prefrontal cortex. The data is BIDS-compatible.
Thank you for your help in advance!