For reasons that aren't interesting, I need to create a slice timing file, rather than a slice order file, to run slice timing correction on some data. However, I found the description of the timing file too abbreviated to know for certain how to build one.
Here's the description from the feat html and the balloon from the feat GUI:
"If a slice timings file is to be used, put one value (ie for each slice) on each line of a text file. The units are in TRs, with 0 corresponding to no shift. Therefore a sensible range of values will be between -0.5 and 0.5."
Here are my questions:
1. I can't infer from the description what the relationship is between sequential lines in the timing file and physical slices in the data.
>> Is it the case that the first line in the file corresponds to the first (i.e., bottom-most) slice in the data, and that the second line in the file corresponds to the second (i.e., one slice above the bottom-most) slice in the data, and so on, regardless of the order in which the slices were collected (ascending, descending, interleaved)?
2. I understand what the sensible range of values is. However, I don't understand how the sign of the values relates to the order in which the slices were collected. I initially assumed that negative values would be used for the early slices and positive values for the later slices, but the slicetimer --tcustom flag says "+ve [positive?] values shift slices forwards in time", which makes me think I may have this backward.
>> Is it the case that negative values should be used for slices collected first, and positive values used for slices collected last?
3. To use a toy example with dummy values, imagine I collect a 5-slice data set in ascending order (so the bottom slice is collected first, and each subsequent slice is one adjacent slice closer to the top of the head).
>> Would a timing file with the proper order and signs be something like this?
-0.50
-0.25
0.00
0.25
0.50
4. Imagine the same toy example, but with the data collected in interleaved ascending order (1,3,5,2,4).
>> Would the timing file be something like this?
-0.50
0.25
-0.25
0.50
0.00
Many thanks,
Ruskin
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