Keith's slice timing for Stella's motor data - maybe wrong source? (see 2 s TR)

tranThesis-KeithSliceTimingFrom20140717

Sorry for the delay. I had to take a crash course in slice timing reconstruction, which is NOT straightforward on the Philips platform.

So, I've managed to reconstruct the files from the 70 TR motor runs with to3d, but only after some nastiness with the file number and slicing order that Philips pukes out. For some odd reason, the time x slice DICOM output failed to generate all of the necessary files (4 IM000 short ) - that took a while to figure out. Additionally, the header information tag was stripped on the Philips output.  Using 2 fields (0020, 0100) and the temporal position identifier - you can suss out the temporal slicing order based on the index of the slice acquisition. However, since the files have to be reindexed, it's not just a matter of advancing through a window to see the offset. This may not be new information to you guys, but it is to me.  From there you just reorder the DICOMs and reconstruct.

The end result is that the temporal slicing is indeed sequential I-to-S with an RAI alignment. The temporal offset per slice is regular. I was able to reconfirm this by checking some older AFNI files as well.

Here's the output:

3dinfo -VERB epi01+orig.
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Sep  6 2013) [64-bit]

Dataset File:    epi01+orig
Identifier Code: XYZ_zvH6dcIR9F2rxNoKw0_AmA  Creation Date: Mon Jul  17 18:51:41 2014
Template Space:  ORIG
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   73,543,680 (74 million [mega]) bytes
Geometry String: "MATRIX(2,0,0,-94.74582,0,2,0,-94.74582,0,0,2,-27.57191):96,96,57"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Anterior-to-Posterior
  third  (z) = Inferior-to-Superior   [-orient RAI]
R-to-L extent:   -94.746 [R] -to-    95.254 [L] -step-     2.000 mm [ 96 voxels]
A-to-P extent:   -94.746 [A] -to-    95.254 [P] -step-     2.000 mm [ 96 voxels]
I-to-S extent:   -27.572 [I] -to-    84.428 [S] -step-     2.000 mm [ 57 voxels]
R-to-L center:     0.254 [L]
A-to-P center:     0.254 [P]
I-to-S center:    28.428 [S]
Number of time steps = 70  Time step = 2.00000s  Origin = 0.00000s  Number time-offset slices = 57  Thickness = 2.000
Time-offsets per slice: 0.000 0.035 0.070 0.105 0.140 0.175 0.211 0.246 0.281 0.316 0.351 0.386 0.421 0.456 0.491 0.526 0.561 0.596 0.632 0.667 0.702 0.737 0.772 0.807 0.842 0.877 0.912 0.947 0.982 1.018 1.053 1.088 1.123 1.158 1.193 1.228 1.263 1.298 1.333 1.368 1.404 1.439 1.474 1.509 1.544 1.579 1.614 1.649 1.684 1.719 1.754 1.789 1.825 1.860 1.895 1.930 1.965