Hi Afni Experts,
I wanted to use custom slicetime file in order to apply physio correction to multiecho data (supply 1D file) and then apply the same pattern to 3dTshift (via afni_proc.py). Additionally I wanted to correct TR in the header.
1) Does RetroTS(or MCRetroTS) uses TR in units of seconds and expects the custom sliceorder to also be in units of seconds (column format)?
I used Opts.SliceOrder='Custom' and Opts.SliceOffset='SliceOrder_columnformat.1D' in units of seconds.
Next step is 3dTshift. When looking at the 3dTshift page the examples of slice timing seems to be in milliseconds:
or example if nz = 5 and TR = 1000, then the inter-slice
time is taken to be dt = TR/nz = 200. In this case, the
slices are offset in time by the following amounts:
S L I C E N U M B E R
tpattern 0 1 2 3 4 Comment
--------- --- --- --- --- --- -------------------------------
altplus 0 600 200 800 400 Alternating in the +z direction
alt+z2 400 0 600 200 800 Alternating, but starting at #1
altminus 400 800 200 600 0 Alternating in the -z direction
alt-z2 800 200 600 0 400 Alternating, starting at #nz-2
seqplus 0 200 400 600 800 Sequential in the +z direction
seqminus 800 600 400 200 0 Sequential in the -z direction
If @filename is used for tpattern, then nz ASCII-formatted numbers
are read from the file. These indicate the time offsets for each
slice. For example, if 'filename' contains
0 600 200 800 400
then this is equivalent to 'altplus' in the above example.
(nz = number of slices in the input dataset)
My original file was in milliseconds (row format) which I converted to seconds (colum format) for RetroTS.
In this example of 3dTshift it looks like the units are in milliseconds, however I thought that this would have to match the units of TR which is 1.5 seconds?
2)Is the header sliceorder info if I supply a 3Ttshift -tpattern @sliceorder file assumed to be in millisec or sec (or is there a way to specify so that it interprets the info correctly)?
3) I used 3drefit to enter TR of 1500msec and still displayed as sec. Does tpattern have to be in units of seconds (since TR shows up as seconds) or keep as msec?
Thanks,
Ajay
