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#!/bin/bash
# Copyright (c) 2008-2025 the MRtrix3 contributors.
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Covered Software is provided under this License on an "as is"
# basis, without warranty of any kind, either expressed, implied, or
# statutory, including, without limitation, warranties that the
# Covered Software is free of defects, merchantable, fit for a
# particular purpose or non-infringing.
# See the Mozilla Public License v. 2.0 for more details.
#
# For more details, see http://www.mrtrix.org/.
set -e
if [ "$#" -eq 0 ]; then
echo "
gen_scheme: part of the MRtrix package
SYNOPSIS
gen_scheme numPE [ bvalue ndir ]...
numPE the number of phase-encoding directions to be included in
the scheme (most scanners will only support a single PE
direction per sequence, so this will typically be 1).
bvalue the b-value of the shell
ndir the number of directions to include in the shell
DESCRIPTION
This script generates a diffusion gradient table according to the
parameters specified. For most users, something like the following would be
appropriate:
gen_scheme 1 0 5 750 20 3000 60
which will geneate a multi-shell diffusion gradient table with a single
phase-encode direction, consisting of 5 b=0, 20 b=750, and 60 b=3000
volumes.
The gradient table is generated using the following procedure:
- The directions for each shell are optimally distributed using a bipolar
electrostatic repulsion model (using the command 'dirgen').
- These are then split into numPE sets (if numPE != 1) using a brute-force
random search for the most optimally-distributed subsets (using the command
'dirsplit').
- Each of the resulting sets is then rearranged by inversion of individual
directions through the origin (i.e. direction vector x => -x) using a
brute-force random search to find the most optimal combination in terms
of unipolar repulsion: this ensures near-uniform distribution over the
sphere to avoid biases in terms of eddy-current distortions, as
recommended for FSL's EDDY command (this step uses the 'dirflip' command).
- Finally, all the individual subsets are merged (using the 'dirmerge'
command) into a single gradient table, in such a way as to maintain
near-uniformity upon truncation (in as much as is possible), in both
b-value and directional domains. In other words, the approach aims to
ensure that if the acquisition is cut short, the set of volumes acquired
nonetheless contains the same relative proportions of b-values as
specified, with directions that are near-uniformly distributed.
The primary output of this command is a file called 'dw_scheme.txt',
consisting of a 5-column table, with one line per volume. Each column
consists of [ x y z b PE ], where [ x y z ] is the unit direction vector, b
is the b-value in unit of s/mm², and PE is a integer ID from 1 to numPE.
The command also retains all of the subsets generated along the way, which
you can safely delete once the command has completed. Since this can
consist of quite a few files, it is recommended to run this command within
its own temporary folder.
See also the 'dirstat' command to obtain simple metrics of quality for the
set produced.
"
exit 1
else
nPE=$1
if [ $nPE -ne 1 ] && [ $nPE -ne 2 ] && [ $nPE -ne 4 ]; then
echo "ERROR: numPE should be one of 1, 2, 4"
exit 1
fi
shift
# store args for re-use:
ARGS=( "$@" )
# print parsed info for sanity-checking:
echo "generating scheme with $nPE phase-encode directions, with:"
while [ ! -z "$1" ]; do
echo " b = $1: $2 directions"
shift 2
done
perm="" #"-perm 1000"
# reset args:
set -- "${ARGS[@]}"
merge=""
while [ ! -z "$1" ]; do
echo "====================================="
echo "generating directions for b = $1..."
echo "====================================="
merge=$merge" "$1
dirgen $2 dirs-b$1-$2.txt -force
if [ $nPE -gt 1 ]; then
dirsplit dirs-b$1-$2.txt dirs-b$1-$2-{1..2}.txt -force $perm
if [ $nPE -gt 2 ]; then
dirsplit dirs-b$1-$2-1.txt dirs-b$1-$2-1{1..2}.txt -force $perm
dirsplit dirs-b$1-$2-2.txt dirs-b$1-$2-2{1..2}.txt -force $perm
# TODO: the rest...
for n in dirs-b$1-$2-{1,2}{1,2}.txt; do
dirflip $n ${n%.txt}-flip.txt -force $perm
merge=$merge" "${n%.txt}-flip.txt
done
else
for n in dirs-b$1-$2-{1,2}.txt; do
dirflip $n ${n%.txt}-flip.txt -force $perm
merge=$merge" "${n%.txt}-flip.txt
done
fi
else
dirflip dirs-b$1-$2.txt dirs-b$1-$2-flip.txt -force $perm
merge=$merge" "dirs-b$1-$2-flip.txt
fi
shift 2
done
echo $merge
dirmerge $nPE $merge dw_scheme.txt -force
fi
|
