Hello, I need to derive the slice acquisition order/ slice timing for some Philips PAR/REC data (I am getting the BIDS validator error relating to this). I’ve read through the informative Heudiconv: no extraction of slice-timing data based on Philips DICOMs post. However, most of it deals with Philips DICOMS, from which you can glean the slice order (even if from UIDs), rather than from PAR files/Philips console report. Other posts and helpful scripts also assume that you either already know the order, or have this in a header file to calculate the slice timing values.
I have some clues as to how to derive order information from the PAR file/ scanner report, but I wanted someone with knowledge on the subject to confirm this (or not).
Relevant fields from the console report:
. Patient position : Head First Supine
. Preparation direction : Anterior-Posterior
. Repetition time [ms] : 2200.000
SENSE = “yes”;
P reduction (AP) = 2.5;
MB SENSE = “no”;
Stacks = 1;
type = “parallel”;
slices = 38;
Slice scan order = “HF”;
TR = “user defined”;
(ms) = 2200;
Temporal slice spacing = “equidistant”;
Packages = 1;
and from the PAR file
slice orientation ( TRA/SAG/COR ) = 1
My assumptions are as follows:
Slice Scan Order = HF= Head-to-foot = Descending, which added to the PAR file
slice orientation = 1, (axial), would mean the order are axial slices descending from head to foot (this is crucial, but only an educated guess).
Packages = 1, looking at the SPM wikibooks entry, this should simply be a descending 4,3,2,1 order.
I am also assuming that this was not a multiband acquisition since MB SENSE is turned off, that “regular” SENSE does not affect slice timing, and that temporal slice spacing = “equidistant” means ther are no temporal gaps.
Hence, it would seem that slice timings would simply be derived from sequentially subtracting the TA (2.2s/38slices) from each slice starting at (but excluding) 2.2s until zero.
@drmclem, could you kindly confirm this? I am making an educated guess on all of this, but would really appreciate confirmation on the console values, as I was not involved in data acquisition, and only have this to go by. Many thanks in advance!!