Software

rapidtide
This is the main suite of programs we use for doing time delay processing.  All programs are in python, and are compatible with python 2 and 3.  The code is being released under the Apache 2.0 license.  The repository is on github (under construction as of June 2016).

getslicetimes
This is a very small program that takes the guesswork out of slice time correction.  It extracts the slice acquisition times from a Siemens mosaic dicom file and prints it to stdout in a format that can be used as an FSL slicetimings.txt file. This is especially useful with multiband acquisitions, where multiple slices are acquired at the same time, and the exact slice acquisition time is difficult to back out.  This utility is a python program (python 2 and 3 compatible) that runs from the command line.  Requires numpy, and pydicom. Link below.  NB: for data acquired with the CMRR multiband sequence versions 008 and earlier, do not use the first image in the series - the header is not properly initialized.  All headers from image 2 onward are correct.

usage: getslicetimes somedicomfile.dcm > slicetimes.txt
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getslicetimes
(3k)
Blaise Frederick,
Jun 16, 2016, 8:07 PM
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