SliceTiming related information in .PAR file

1

Dear experts,

Im now trying to perform SliceTimingCorrection during preprocessing fMRI data using fMRIprep.

I have some relevant information about Slices acquired during scan in PAR file.

In PAR file, There is slice number information and it says 35,33,31,29…,34,32,30…2.(In case total slice number is 35).

And There is also index_in_REC, I assume that this index tell when slices are scanned.

According to these info(slice number, index_in_REC), I assume that slice number 35 was scanned first and so on.(slice number 2 scanned last if I’m correct)

So, I decided to add SliceTiming information accordingly.

35 slice as index 0, 33 as index 1, 31 as index 2,…4 as index -2, 2 as index -1.

Here I attach python codes I used to calculate SliceTiming information.

‘’’
if n_slices % 2 == 0:
even = list(range(n_slices, 0, -2))
odd = list(range(n_slices - 1, 0, -2))
slice_order = even + odd
else:
odd = list(range(n_slices, 0, -2))
even = list(range(n_slices - 1, 0, -2))
slice_order = odd + even

# Create slice timing list in slice-number order (index = slice_num - 1)
slice_timing = [0] * n_slices
for i, slice_num in enumerate(slice_order):
    slice_timing[slice_num - 1] = round((i) * (3 / n_slices), 4)  # round for JSON compatibility

‘’’

If u know anything about this issue, please gimme some advice.

P.S) Im using Philips Scanner.

Sincerely,

Junyong Oh

2

You can not determine many details, including slice timing from Philips PAR/REC files, which was built in simpler times. The slice number allows you to reorder slices as saved to disk to their position in the volume. Be aware that PAR/REC files often save images to disk in a jumbled order, presumably reflecting their delivery from a parallel reconstruction system. Wikibooks has some general guidelines for determining slice time for Philips scanners, but this will require you to know settings of the sequence from the scanner console and pre-dates modern multi-band sequences. The Philips Clinical Scientist affiliated with your instrument is the ideal person to guide you through the process of determining these details.