maxpietsch

/* Copyright (c) 2008-2022 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

maxpietsch

#!/usr/bin/env bash
set -x

tmp_dir=$(mktemp -d -t mrregister_init-XXXXXXXXXX)
cd $tmp_dir
echo $tmp_dir

# ____ 0. get DWI data and create two ODFs ____
for sub in sub-02 sub-03; do
wget --quiet https://github.com/MRtrix3/script_test_data/raw/master/BIDS/"${sub}"/dwi/"${sub}"_dwi.bval

maxpietsch

#!/usr/bin/env python


def usage(cmdline):
  cmdline.set_author('Max Pietsch')
  cmdline.set_synopsis('Landmark-based manual alignment')
  cmdline.add_description('Calculates the rigid transformation between two images based on three or more matching landmarks.')
  cmdline.add_argument('fixed', help='The reference input image')
  cmdline.add_argument('moving', help='The moving input image')
  cmdline.add_argument('rigid', help='The output transformation')

maxpietsch

#! /usr/bin/env python3

# check subject ID for validity.
usage="""
usage:

is_valid_id.py <dhcp_subject_id>

example: ./is_valid_id.py CC01253XX08

maxpietsch

#!/usr/bin/env python
#
#   generate screenshots for QC report
#
#
#   Author:  Max Pietsch
#            King's College London
#            maximilian.pietsch@kcl.ac.uk
#

maxpietsch

#/bin/env bash

do_nonlinear_registration=false

tmp_dir=$(mktemp -d -t tcktransform-XXXXXXXXXX)
cd $tmp_dir

# ____ 0. get DWI data and create two ODFs ____
for sub in sub-02 sub-03; do
wget --quiet https://github.com/MRtrix3/script_test_data/raw/master/BIDS/"${sub}"/dwi/"${sub}"_dwi.bval

maxpietsch

#!/usr/bin/env python3

# tool to visualise angular and l=0 dependency of multiple MRtrix3 response functions
# Author: Maximilian Pietsch

import argparse
import numpy as np
from scipy.special import sph_harm
import matplotlib.pyplot as plt

maxpietsch

/* Copyright (c) 2008-2020 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

maxpietsch

#!/usr/bin/env bash
APP=mrview
mkdir -vp ${APP}.app/Contents/MacOS ${APP}.app/Contents/Resources
PATH="$PATH:/usr/libexec" # PlistBuddy in PATH
printf '#!/usr/bin/osascript\ntell application "Terminal"\n\tactivate\n\tdo script "mrview; exit"\nend tell\n' > ${APP}.app/Contents/MacOS/${APP}
chmod +x ${APP}.app/Contents/MacOS/${APP}
PlistBuddy ${APP}.app/Contents/Info.plist -c "add CFBundleDisplayName string ${APP}"
PlistBuddy ${APP}.app/Contents/version.plist -c "add ProjectName string ${APP}"

maxpietsch