sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
e6b2079fae25f0eb800fcc1d22d9eb4cb08693b335de284373008f40b3169e58 | Shell | 5,014 | 150 | # @todo - better / more robust parsing of inputs from env vars.
## -------------------
## Constants
## -------------------
# @todo - apt repos/known supported versions?
# @todo - GCC support matrix?
# List of sub-packages to install.
# @todo - pass this in from outside the script?
# @todo - check the specified subp... |
bdead1288410b084fd00509339ac85e4b78b121a2ea53a5928c4685f3f823319 | Shell | 5,019 | 138 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
command_line_specified_study_folder=""
command_line_specified_subj=""
command_line_specified_run_local="FALSE"
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argument=... |
ccd6004d824bf4cca9d255b78ec72914e6d3a6a3c02b723ba5cdd168f63f6fa4 | Shell | 5,081 | 122 | #!/bin/bash
set -e
# WCH RSSI Project 2025-11-29
# We want RSSI lesion masks to be in 3D T1w space for further analysis.
# Input arguments
BIDS_DIR=$1
SUBJECT_ID=$2
SESSION_ID=$3
# Flags
have_dwi_lesion_mask=false
have_t1w_lesion_mask=false
have_mni_lesion_mask=false
#
lesion_mask_dir="${BIDS_DIR}/derivatives/lesi... |
81b67d4037bd9f25541b4342b599be2e02c6ccbeaf5d2172b8c9fceb638d82a3 | Shell | 5,084 | 137 | #!/bin/bash
subject=$1
algostr=$2
outputdir=$3
set -e
set -x
if [ $USER = "ubuntu" ]; then
#studydir=/home/ubuntu/mniwarp
scriptdir=/home/ubuntu
export FSLDIR=$HOME/fsl
export FSLOUTPUTTYPE=NIFTI_GZ
export PATH=${FSLDIR}/bin:${PATH}
export MRTRIXDIR=$HOME/mrtrix3
export PATH=${MRTRIX... |
d8699502c27eb9d0da1d0444c8c83c44bf29ee3a30fe165496cf30df00c0b639 | Shell | 5,180 | 138 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
g_matlab_d... |
37bde79bb290a1c7a1666c1ffb95c8237c12573d9f7df15cff06a41b0d3c84d7 | Shell | 5,243 | 113 | #!/bin/bash
# PediatricOpenTargets 2022
# Eric Wafula
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
... |
a4ba5118797b5e284c0b52418ee5ef1cd14fb40393b9a3acff885b138db3f3fa | Shell | 5,298 | 95 | #!/bin/bash
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
# Module author: Sangeeta Shukla, Alvin... |
90179ff9729d339ce64d4752b526ceb40826c331356b8d030dbb5ba6596b5cf8 | Shell | 5,374 | 138 | #!/usr/bin/env bash
# Dry-run validation matrix for the FIRE manifest and reference handling.
# Run with the working directory set to fire-test-data (see the test-dry pixi task).
set -uo pipefail
SNAKEFILE="$PIXI_PROJECT_ROOT/workflow/Snakefile"
CFG="$PIXI_PROJECT_ROOT/tests/config"
FAILURES=0
snk() {
snakemake -... |
f6de14c38dad074807f655a670da59ee0e3053b7809fb1e3ceb93126c18ec563 | Shell | 5,382 | 120 | #
# mexopts.sh Shell script for configuring MEX-file creation script,
# mex, to use NVCC for building GPU MEX files.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. No ... |
f2c92d9df850b9dbe4c75373a9f0b81ad98679a1a5b371eac4d991ca21cabd33 | Shell | 5,438 | 81 | #!/bin/bash
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
script_name=$(basename "${0}")
show_usage() {
cat <<EOF
${script_name}: Sub-script of GenericfMRISurfacePr... |
d553123d560b6d34df84c1d8f01a7978a18bac4773640a75141440d26f00a595 | Shell | 5,528 | 164 | #! /bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Andreas Schuh
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the A... |
9899e2ba9424311bfc8f89dc19cdfa4934eb60e1bebb574d2d599dbaf6070eec | Shell | 5,544 | 112 | #!/bin/bash
# K S Gaonkar
# This analysis applies the TP53 inactivation classifier https://linkinghub.elsevier.com/retrieve/pii/S2211124718304376
# NF1 inactivation classifier https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3519-7
# Predicts TP53 and NF1 inactivation score per polya and stranded RN... |
b6f9364b260c3c9594fe8d56bbf9a063ace6eba5fca6f13d20c1f1b0c6ed96f9 | Shell | 5,549 | 92 | #!/bin/bash
#SBATCH --job-name=setup_KR4SL
#SBATCH --output=./slurm_out/setup_KR4SL.out
#SBATCH --error=./slurm_out/setup_KR4SL.err
#SBATCH --time=12:00:00
#SBATCH --mem=64Gb
#SBATCH -c 4
#SBATCH --gres=gpu:1
#SBATCH -p gpu_p
#SBATCH --qos=gpu_normal
# To run this file:
# cd ./reproduce/synleth/
# sbatch ./scripts/00_... |
36e9dac58d4a6f8bea9e7960041a0e589395ac835f671b79c3ad74cb22274b73 | Shell | 5,569 | 145 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL
# environment: HCPPIPEDIR, FSLDIR
# ------------------------------------------------------------------------------
# Usage Description Function
# ------------------------------------------------------------------------------
set -eu
pipedirg... |
6215c8c131bda618305ae12e21af8e554e69118bdf7aff8764618bb63fc6e5c1 | Shell | 5,600 | 170 | #! /bin/bash
# brief: Import various CNN models from the web
# author: Andrea Vedaldi
# Models are written to <MATCONVNET>/data/models
# You can delete <MATCONVNET>/data/tmp after conversion
CAFFE_URL=http://dl.caffe.berkeleyvision.org
CAFFE_GIT=https://github.com/BVLC/caffe/raw
VGG_URL=http://www.robots.ox.ac.uk/~vg... |
08809a21bc0eb37770a9b54665161f59dbf40c917630d3283e94e62c8162a872 | Shell | 5,609 | 128 | #!/bin/bash
PROJECT=/Volumes/Elements_CR/atrialmtk/src/3Processing/UAC_Codes
DATA="/Volumes/Elements_CR/atrialmtk/Examples/Example-Biatrial-MRI/3Processing"
ConvertFilesLoc=/Volumes/Elements_CR/atrialmtk/src/3Processing/UAC_Codes
PVLabelT=0.8
LAALabelT=0.35
UnitsRescale=1000
index=1
export PYTHONPATH=$PROJECT
ES_d... |
bf8d2d09c87c01ac8601febb28db2ab9f6ee91cf92d909bd1ee311dd523a1c3f | Shell | 5,619 | 131 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=01:00:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
# Adapted from Marc Jaskir's exce... |
01ad32003e41b2b01f24f806e088a6a21f2622a7f1f46446e3ef0f736f9f7bdd | Shell | 5,639 | 181 | #!/bin/bash
# ==============================================================================
# start_mcp_server_interactive.sh
#
# Start the ChemGraph MCP server on an ALCF compute node via HTTP.
#
# Usage (after getting an interactive session via qsub -I):
# ./start_mcp_server_interactive.sh [OPTIONS]
#
# Options:
#... |
1ccecc4eca0fe4f7fa477b3c1f4973a1a0bdbb620b5446048a6234e6eacd83d7 | Shell | 5,639 | 215 | #!/usr/bin/env bash
set -eu
SCRIPT_DIR="$(dirname "$0")"
fail() {
printf >&2 "%s: %s\n" "$0" "$1"
exit 1
}
wait_for_db() {
wait-for-it "${CVAT_POSTGRES_HOST}:${CVAT_POSTGRES_PORT:-5432}" -t 0
}
wait_for_redis_inmem() {
wait-for-it "${CVAT_REDIS_INMEM_HOST}:${CVAT_REDIS_INMEM_PORT:-6379}" -t 0
}
wa... |
b7d57eaa73ade0cc8001007349970293c1c90e51b3a6883ff71ca3b03568937b | Shell | 5,650 | 207 | #!/bin/bash
set -e
function usage()
{
cat << EOF
Usage: run_lit_containerized.sh --input_image <input_t1w_volume> --mask_image <lesion_mask_volume> --output_directory <output_directory> [OPTIONS]
run_lit_containerized.sh takes a T1 full head image and creates:
(i) an inpainted T1w image using a lesion mask
... |
03ea9543de5dfff32bbbc57b5a5b9674386b6478368716f03857385763b7e27d | Shell | 5,690 | 201 | #!/usr/bin/env bash
# Runs all C++ examples
set -Eeuo pipefail
# Function to print the script's synopsis
print_synopsis() {
echo "Usage: $(basename "$0") [-d] [--with=example] [prefix]"
echo " -d Toggle distributed mode (optional). Does not expect result"
echo " files to be ... |
f363f305dfdb77a6ca16b37abd718dc699025858ae9ac84f3c3d35265c01555c | Shell | 5,747 | 115 | #!/bin/bash
PROJECT=/Volumes/Elements_CR/atrialmtk/src/3Processing/UAC_Codes
DATA="/Volumes/Elements_CR/atrialmtk/Examples/Example-LeftAtrium/3Processing"
ConvertFilesLoc=/Volumes/Elements_CR/atrialmtk/src/3Processing/UAC_Codes
PVLabelT=0.7
LAALabelT=0.25
UnitsRescale=1000
index=1
export PYTHONPATH=$PROJECT
LAendo... |
b758ea4cb1222ec22ebce97b47d0ef59ff71c139a133028b47fb686b78bb8b0c | Shell | 5,793 | 178 | #!/bin/bash
#Customize multibuild logic that is run after entering docker.
#Sourced by docker_build_wrap.sh and docker_test_wrap.sh .
#Runs in Docker, so only the vars passed to `docker run' exist.
#See multibuild/README.rst
echo "=== Loading config.sh === "
# To see build progress
function build_wheel {
build_b... |
871fad9bc77b0383f53c41345d5d5e6259760445d12969d253090368e548c6f8 | Shell | 5,797 | 188 | #!/bin/bash
# ==============================================================================
# start_mcp_server_interactive.sh
#
# Start the ChemGraph XANES MCP server on a compute node via HTTP
# during an interactive session.
#
# Usage (after getting an interactive session via qsub -I or locally):
# ./start_mcp_ser... |
ef74f9eadf32e7601c3b477ee4a39a66d3c974b447f10d3b78266a7c74892db6 | Shell | 5,804 | 220 | #!/bin/bash
#set -xv
# Global default values
DEFAULT_STUDY_FOLDER="${HOME}/data/HCPpipelines_ExampleData"
DEFAULT_SUBJECT_LIST="100307 100610"
DEFAULT_ENVIRONMENT_SCRIPT="${HOME}/projects/HCPpipelines/Examples/Scripts/SetUpHCPPipeline.sh"
DEFAULT_RUN_LOCAL="FALSE"
#
# Function Description
# Get the command line optio... |
874d12910150770786d792a4873afc1480e6dd6db69302799e24684d1baa6c96 | Shell | 5,810 | 110 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=01:00:00
#SBATCH --job-name=decoding_group
#SBATCH --output=/imaging/hauk/rl05/fake_diamond/scripts/analysis/neural/decoding/job_log/job_output.log
#SBATCH --error=/imaging/hauk/rl05/fake_diamond/scripts/analysis/neural/decoding/job_log/job_error.... |
996f4dd9f82995e54801cf8e5050653d84806f6eab7bee37f8ea9d1e9ea5fe52 | Shell | 5,811 | 87 | ###### Subject list and path
subjlist='/data/users/wliu/demo_dHCP_Analysis/TermList_myelin.txt'
for s in $(cat $subjlist)
do
if [[ $s == CC* ]]
then
subj=$s
continue
else
sess=$s
fi
subjid=$subj
session=$sess
WorkbenchBinary='/opt/workbench/exe_rh_linux64/wb_command' #path of Workbench
VolumePath=/data/data/dHCP/dHC... |
0510c8a2e2a37eb2246f9b4a87cd4ddaa5c4a9965c67c67d4be5b6a0a87b26e7 | Shell | 5,813 | 126 | #!/bin/bash
source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@" # Debugging functions; also sources log.shlib
echo -e "\n START: run_topup"
workingdir=$1
topup_config_file=$2
# Optional 3rd arg: SPECIES (defaults to Human; matches PreFreeSurfer/FreeSurfer convention)
SPECIES=${3:-Human}
# Derive SpeciesLabel from... |
ae23071e6f0457315a51e6a66c45962e1856858f3ee73eb435b1c71acc16d262 | Shell | 5,833 | 139 | #!/bin/bash
command_line_specified_run_local=FALSE
while [ -n "$1" ]; do
case "$1" in
--runlocal) shift; command_line_specified_run_local=TRUE ;;
*) shift ;;
esac
done
#################################################################################################
# General input variables
##... |
b978db4b4ea6faf59e25ad7d2966ca7b930f8b834ac1634a3166480b8f6bbeed | Shell | 5,854 | 113 | #!bin/bash
NC="\e[39m"
BLUE="\e[34m"
GREEN="\e[32m"
RED="\e[31m"
subjects_list=$1
subjects=( $(cat $subjects_list) )
root_dir=`pwd`
source_dir=$2
echo -e "${BLUE}######################################"
echo -e "##### Starting Bullseye Pipeline #####"
echo -e "######################################${NC}"
echo -e "${... |
550430d07c16ef89c31567e1c4a83d5a09e9a74312aa6e32c60f5473dbfd79e5 | Shell | 5,863 | 91 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/eval/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/eval/sl... |
2f6d4df85dc90c91d706de7cdfdba13548726a62cc9deb9b0222cc722d72fddb | Shell | 5,898 | 147 | #!/bin/sh
set -e
set -o pipefail
printf "Start generating pre-release files...\n\n"
# Set locations for s3 bucket that contains release files
URL="s3://d3b-openaccess-us-east-1-prd-pbta/open-targets"
RELEASE="v13"
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# If RU... |
a57c207cdf3ddca28d6668deaba57e40227e440e0105dea155318da43de60d15 | Shell | 5,927 | 316 | #!/bin/bash
declare -a s1
s1[21]=245
s1[22]=277
s1[23]=251
s1[24]=258
s1[25]=243
s1[26]=262
s1[27]=248
s1[28]=320
s1[29]=244
s1[30]=243
s1[31]=242
s1[32]=304
s1[33]=241
s1[34]=249
s1[35]=242
s1_nv[21]=190543360
s1_nv[22]=215430656
s1_nv[23]=195209728
s1_nv[24]=200653824
s1_nv[25]=188987904
s1_nv[26]=203764736
s1_nv[27... |
e9b1d9c1aa9cc369342cb1287d4a6054afa16d91844436e872f0e7433d1215c3 | Shell | 5,952 | 130 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
opts_SetScriptDescription "average initial transmit field files ... |
ef08e9d9b4e608303d72ea3c55f4e49a416c4ed51d1a0d89c3d342cd26bb4a7f | Shell | 5,973 | 183 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
command_line_specified_study_folder=""
command_line_specified_subj=""
command_line_specified_run_local="FALSE"
command_line_specified_Tasklist=""
command_line_specified_SpecSessionlist=""
local index=0
local numArgs=${#argument... |
7e51cc6b7c2eb78ace91cad42dacebdee4ed9154bc06156484ee1587b0f18b7a | Shell | 5,979 | 154 | # Chante Bethell for CCDL 2019
# Run 01-plot-oncoprint.R
#
# Usage: bash run-oncoprint.sh
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- ... |
d62bbe73caf6f282f297aa786ac3eb75b80af1286b5758aa3c6512d854d0f8f7 | Shell | 6,004 | 127 | #!/bin/bash
python_path=/home/abnousa/software/python3.6.5/bin/python #should have pysam, pybedtools installed. bedtools, samtools should be in the path
Rscript_path=/opt/R-3.4.3/lib64/R/bin/Rscript
###################################################################
feather=1 #start from feather or run only MAPS
maps=0... |
3421609a6dbc76da0f50641a93aacdfd2e6d26cdc4b8a33c184494d07821919c | Shell | 6,030 | 114 | # train replicates of distilled ResidualBind models that predict mean+aleatoric+epistemic
### script params/variables
N_MODS=10 # nr. of distilled models to train
MODELS_DIR=../results/distilled_lentiMPRA_epistemic # path to output directory
DATA_DIR=../data/lentiMPRA # path to directory with lentiMPRA data
CONFIG=..... |
17e7689e19d5ad17f680951ad39b7b60c30db091be5aa5698946b2d3fad88ca7 | Shell | 6,052 | 183 | #!/bin/bash
#
# # Compile_All_MATLAB_code.sh
#
# Compile all the MATLAB source code used in the HCP Pipelines code base
#
# ## Copyright Notice
#
# Copyright (C) 2019 The Connectome Coordination Facility (CCF)
#
# ## Author(s)
#
# * Timothy B. Brown, Neuroinformatics Research Group, Washington University in St. Louis
... |
61287478c4da15a8f1bd3353ed3b946f49c8435d46d3328652bca2846c9a67c4 | Shell | 6,058 | 163 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL, Connectome Workbench (wb_command)
# environment: HCPPIPEDIR, FSLDIR, CARET7DIR
########################################## PIPELINE OVERVIEW ##########################################
# TODO
########################################## OUTPUT ... |
caead5e0b8fb9e9a7b2bb45ef1e6ef4cd452360253782fd8cb5397974ecf4fb4 | Shell | 6,079 | 157 | #!/bin/bash
# IntensityCorNHP.sh
# Intensity bias correction and normalization in NHP
# Takuya Hayashi, RIKEN BCIL 2016-2024
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
#fix this if the script is more than one level below HCPPIPEDIR
export HCPPIPEDIR="$(dirname -- "$0")... |
58902729cbd5d90bb54fddbc12eaa2cb13610fd95258cbc3fcc8c20b512b2fc7 | Shell | 6,080 | 210 | #!/usr/bin/env bash
set -euo pipefail
if [ "$#" -lt 3 ]; then
echo "Usage: bash fmriprep_single.sh <bids_dir> <subject_id> <session_id> [license_file]"
exit 1
fi
bids_dir="$1"
subject_id="$2"
session_id="$3"
license_file="${4:-/home/lxg/license.txt}"
fmriprep_dir="${bids_dir}/derivatives/fmriprep"
work_dir="${b... |
192a1ebe2cb9aa40397b37f4d96eac6298ebafffefcf87b6e6085a48a727b214 | Shell | 6,100 | 179 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
command_line_specified_study_folder=""
command_line_specified_subj=""
command_line_specified_run_local="FALSE"
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argument=... |
db53cd950557e78575718d74b691b50dccf8e4d58977eb0b34201d5dbd814a17 | Shell | 6,132 | 86 | #!/bin/bash
# Define paths
ROOT=/home/user/Documents/fMRI_Exp
FSLDIR="/home/user/fsl"
for subject in {11..12}; do
cur_subject=$subject
if [ "$subject" -lt 10 ]; then
cur_subject="0${subject}"
echo "add zero"
fi
echo "cur_subject is ${cur_subject}"
FUNC_IMAGE=/home/user/Documents/fMRI_Exp/example_func_all_... |
2384ea9a03b8b66d7e886b66b90d60d7971d7bceb976e97a90d945ff570d8308 | Shell | 6,136 | 156 | #!/bin/bash
# ------------------------------------------------------------------------------
# Usage Description Function
# ------------------------------------------------------------------------------
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
#fix this if the script ... |
0e262c8e33cb98f961a8ca35fca0283f1a52c574e3534811630a4ebfeccb1ac3 | Shell | 6,173 | 96 | ###### Subject list and path
subjlist='/data/users/wliu/demo_dHCP_Analysis/TermList_myelin.txt'
for s in $(cat $subjlist)
do
if [[ $s == CC* ]]
then
subj=$s
continue
else
sess=$s
fi
subjid=$subj
session=$sess
WorkbenchBinary='/opt/workbench/exe_rh_linux64/wb_command' #path of Workbench
StandardSpherePath=/data/users... |
18a34804800ad04edab57eb193b5c1b9d055b7b51009b1c9160b8bdfcfaeac45 | Shell | 6,183 | 165 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
command_line_specified_study_folder=""
command_line_specified_subj=""
command_line_specified_run_local="FALSE"
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argument=... |
b17c4a94319a9457029e7a29e67b7bbb7977f4f72c78813ea448cb4bbefc5e85 | Shell | 6,241 | 320 | #!/bin/bash
declare -a s1
s1[21]=245
s1[22]=277
s1[23]=251
s1[24]=258
s1[25]=243
s1[26]=262
s1[27]=248
s1[28]=320
s1[29]=244
s1[30]=243
s1[31]=242
s1[32]=304
s1[33]=241
s1[34]=249
s1[35]=242
s1_nv[21]=190543360
s1_nv[22]=215430656
s1_nv[23]=195209728
s1_nv[24]=200653824
s1_nv[25]=188987904
s1_nv[26]=203764736
s1_nv[27... |
f86ce3312f421bd0d232c5c980819cb7da0bdb9cdcc25028b67a60512ef12987 | Shell | 6,258 | 206 | #!/bin/sh
# [description]
# Prepare a source distribution of the R-package
# to be submitted to CRAN.
#
# [arguments]
#
# --r-executable Customize the R executable used by `R CMD build`.
# Useful if building the R-package in an environment with
# non-standard builds of... |
6feeb872d5739fd9c34bf0193c93351b6ebd9e2631c15df74961ffa1f5ad1d8a | Shell | 6,285 | 120 | # train replicates of distilled MPRAnn models w/ activity+epistemic+epistemic predictions
### script params/variables
N_MODS=10 # nr. models to train
MODELS_DIR=../results/distilled_MPRAnn_epistemic # path to output dir
DATA_DIR=../data/MPRAnn_aleatoric # path to directory with data
CONFIG=../config/MPRAnn.yaml # pa... |
159d091b504936321d175871e808d3ce6cdaafe4ac71b5235971a48385a70f96 | Shell | 6,304 | 172 | #!/usr/bin/env bash
#
# convert_keras_model.sh
#
# Converts a legacy Keras/TensorFlow SavedModel directory
# (containing assets/, keras_metadata.pb, saved_model.pb, variables/)
# into a Keras 3 native ".keras" model file.
#
# Usage:
# ./convert_keras_model.sh /path/to/model_folder [output_name.keras]
#
# Requirements... |
28ed524291dfa3d3073cfcf58fc0067ad256467b2d251e4935c1e5b66e391cc3 | Shell | 6,345 | 155 | #!/bin/bash
NC="\e[39m"
BLUE="\e[34m"
GREEN="\e[32m"
RED="\e[31m"
# Parameters
subject_id=$1 # Single subject
source_dir=$2 # Code path
SUBJECTS_DIR=$3 # freesurfer SUBJECTS_DIR
output_dir=$4 # Output path
root_dir=$(pwd)
echo -e "${BLUE}######################################"
echo -e "###... |
14d761591851f76b768170e9ab293409e96d9067554cdeb456891a1925932e08 | Shell | 6,366 | 159 | #!/bin/bash
set -euE
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/tempfiles.shlib" "$@"
opt... |
c4136dce3972d7f6dcc214c458072fb78a717015729d8c1374256e2664752867 | Shell | 6,374 | 118 | # train replicates of distilled ResidualBind models w/ activity+epistemic+epistemic predictions
### script params/variables
N_MODS=10 # nr. of models to train
MODELS_DIR=../results/distilled_ResidualBind_epistemic # path to output dir
DATA_DIR=../data/lentiMPRA_aleatoric # path to directory with data for training
C... |
67212dd69249a41143f21bc5b888d1936da9e2be752c5a08aeb29d47927c8aab | Shell | 6,384 | 149 | #!/usr/bin/env bash
#
# One-command auto-build for VVDViewer on macOS / Linux.
#
# Downloads and builds every third-party dependency (EXCEPT the Vulkan SDK)
# from source via vcpkg, then configures and builds VVDViewer with CMake.
# All dependencies are linked statically except wxWidgets (dynamic). On Linux,
# the syst... |
9d876ec452d08250fd5f05e16866d813c02af10c683f074ba40a3f28ca687cd5 | Shell | 6,413 | 135 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL, Connectome Workbench (wb_command)
# environment: HCPPIPEDIR, FSLDIR, CARET7DIR
# ------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------... |
5df1367b4ce1a81b2dfadade10d10fb256bc8457f91f7f8c15479eb903353a21 | Shell | 6,419 | 318 | #!/bin/bash
declare -a s1
s1[21]=245
s1[22]=277
s1[23]=251
s1[24]=258
s1[25]=243
s1[26]=262
s1[27]=248
s1[28]=320
s1[29]=244
s1[30]=243
s1[31]=242
s1[32]=304
s1[33]=241
s1[34]=249
s1[35]=242
s1_nv[21]=190543360
s1_nv[22]=215430656
s1_nv[23]=195209728
s1_nv[24]=200653824
s1_nv[25]=188987904
s1_nv[26]=203764736
s1_nv[27... |
bee0d1785cded5a181ed9e20f7a5c30306e12a1b2dbc8cf58cb1253e1ea2fd0f | Shell | 6,458 | 271 | #!/bin/bash
set -e
function usage() {
cat << EOF
Usage: run_lit_containerized_custom.sh \
--input_image <input_t1w_volume> \
--mask_image <lesion_mask_volume> \
--output_directory <output_directory> \
--lit_data_dir <lit_data_dir> \
[--output_image <output_image>] \
[OPTIONS]
This script runs LIT inside ... |
8cae29809f05847c1654d92a14b6b974ccbac961f94a0d25196d02f17f92e1a3 | Shell | 6,474 | 132 | #!/usr/bin/env bash
set -euo pipefail
if [ "$#" -ne 8 ]; then
echo "Usage: bash run_ARTS_quick.sh <subject_id> <age> <sex> <synthseg.nii.gz> <wmh_mask.nii.gz> <fa_mni.nii.gz> <output_dir> <mni_to_iit_warp.nii.gz>" >&2
exit 1
fi
SUBJECT="$1"
AGE="$2"
SEX="$3"
SYNTHSEG_IN="$(realpath "$4")"
WMH_IN="$(realpath "$5")... |
8842fe11ae6556fb37820f56b1d30c0f69c568cedd3fdc42cd3f94591bd6dbec | Shell | 6,486 | 191 | #!/bin/bash
set -e
# Requirements for this script
# installed versions of: FSL6.0.4 or higher , FreeSurfer (version 6.0 or higher) , gradunwarp (python code from MGH)
# environment: FSLDIR , FREESURFER_HOME , HCPPIPEDIR , CARET7DIR , PATH (for gradient_unwarp.py)
Usage () {
echo "$(basename $0) --StudyFolder=<p... |
03f05219a8a182b55e15521d39d9742daa19c735efd3e29d40682524bda7c2d1 | Shell | 6,490 | 244 | #!/usr/bin/env bash
set -euo pipefail
# ------------------------ Usage & argument parsing ------------------------ #
if [ "$#" -ne 18 ]; then
echo "Usage: $0 \\"
echo " <preproc_dwi.mif> <dwi_mask.mif> <output_dir> <aseg.nii.gz> \\"
echo " <wm_response.mif> <wm_fod.mif> <wm_fod_norm.mif> \\"
echo " <gm_re... |
fd846a504f140c262fe83431aff68fc2d5d8decf65e11db6413099c05fa00105 | Shell | 6,508 | 100 | #!/bin/bash
PROJECT=/Volumes/Elements_CR/atrialmtk/src/3Processing/UAC_Codes
DATA="/Volumes/Elements_CR/atrialmtk/Examples/Example-Biatrial-CT-shape-model/3Processing"
export PYTHONPATH=$PROJECT
UnitsRescale=1000
cp "$PROJECT/laplace_files/carpf_laplace_alpha.par" "$DATA/LA_vol/carpf_laplace_alpha.par"
cp "$PROJECT... |
5b5ec9048e13009c3ff212fa5c9ead6e5b638f3754759accb6e01972d73624b3 | Shell | 6,530 | 274 | #!/usr/bin/env bash
COMPOSITES=(
epsilon_gamma_box
epsilon_plus
epsilon_plus_flat
epsilon_alpha2_beta1
epsilon_alpha2_beta1_flat
)
ABSCOMPOSITES=(
guided_backprop
excitation_backprop
deconvnet
)
ATTRIBUTORS=(
smoothgrad
integrads
gradient
)
EXTRA=(
occlusion
)
ALLNA... |
4aec693f00bdfe7fcad95b61e373fd5e7ecb790172b541ba394cecbdb4fce3a8 | Shell | 6,574 | 152 | #!/bin/bash
# Define directory paths
GWAS_TOOLS=/Xcan/summary-gwas-imputation/src # Summary GWAS imputation tools
MRI=/TWAS/brain_data/brain/txt_xcan # Input MRI GWAS summary statistics
DATA=/Xcan/cad_data/data # Reference data directory
OUTPUT=/Xcan/mri_output/ ... |
6e9c9adcb60233994255ad7a2305d8d5a41d932e9d36f6d176ec9f0f38df6c4b | Shell | 6,579 | 186 | #!/bin/bash
set -eu
#environment configuration
queue="long.q"
EnvironmentScript="${HOME}/projects/HCPpipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script
#data location
subjects=(123456 654321)
StudyFolder="${HOME}/projects/YA_HCP_Final"
GroupName="HCP_S1200"
#general settings
#identifier for... |
7d89f76b33468d0c572314bbb54e93acc3def9abf87b2d7fa13b0bbb325bbbd2 | Shell | 6,580 | 166 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
g_matlab_d... |
ede6e131751d415c5e136218dd994d5ba791c95c72ab6e84bb77bea4ec463f90 | Shell | 6,606 | 128 | # train an ensemble of lentiMPRA models with aleatoric uncertainty prediction
### script params/variables
ENSEMBLE_SIZE=10
OUTDIR=../results/lentiMPRA_aleatoric
DATA_DIR=../data/lentiMPRA
CONFIG=../config/lentiMPRA.yaml
PROJECT_NAME=lentiMPRA_ensemble_aleatoric
DOWNSAMPLE_ARR=( 0.1 0.25 0.5 0.75 ) # used if downsampl... |
3e7544a6ceff771b60975bf4cc4fa4117a2f2c793faefe142ac27caba35a3f86 | Shell | 6,614 | 215 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # Compile_MATLAB_code.sh
#
# Compile the MATLAB code necessary for running the ICAFIX Pipeline
#
# ## Copyright Notice
#
# Copyright (C) 2019 The Connectome Coordination Facility (CCF)
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford Univ... |
ee3af847e0de483273fdf4cbbf36685b5a6fb7dfcbe5d161eb54a1355e55858d | Shell | 6,641 | 148 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL
# environment: HCPPIPEDIR, FSLDIR
# ------------------------------------------------------------------------------
# Usage Description Function
# ------------------------------------------------------------------------------
set -eu
pipedir... |
95ccfa12da16fbbed07431fff38ee7013eb7784ce34f8bc27546311c1c27f168 | Shell | 6,656 | 190 | #!/bin/bash
set -e -E -u -o pipefail
# defaults
IN_UBUNTU_BASE_CONTAINER=${IN_UBUNTU_BASE_CONTAINER:-"false"}
SETUP_CONDA=${SETUP_CONDA:-"true"}
ARCH=$(uname -m)
if [[ "${ARCH}" == "ppc64le" ]]; then
# no additional setup needed... everything is already bundled in the CI image
exit 0
fi
if [[ $OS_NAME == "... |
7227648f333171de4ba9fa9788acdf6fe2706bd6e22fe6ac299c0ccab8a508cc | Shell | 6,711 | 181 | #! /bin/bash
# IntensityNormalizeNHP.sh
# Normalize intensity of cortical grey or white matter of input volumes
# Takuya Hayashi, RIKEN Brain Connectomics Imaging Laboratory, 2024
# set -eux
Usage () {
echo "Normalize intensity of cortical grey or white matter of input volumes"
echo ""
echo "Usage: $(basename $0) <in... |
4362a8b51c5060459e6595dc3163f9d0999538d857d92af3f2aa788cff734fde | Shell | 6,788 | 115 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL
# environment: HCPPIPEDIR, FSLDIR
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
set -eu
piped... |
e7fd2acce761a3d67760424e2b1c60278f894a5fa11489d3043ba541c20d5500 | Shell | 6,844 | 190 | #!/bin/bash
# 设置错误捕捉，发生错误时打印错误信息并继续执行
trap 'echo "Error occurred at line $LINENO"' ERR
# 使用sobtop生成小分子（*.mol2）所需的gro，top，以及itp文件
# sobtop下载地址：http://sobereva.com/soft/Sobtop/
preprocess_mol() {
mol_file_path=$1
mol_file_dir=$2
mol_name=$3
tgt_dir="$mol_file_dir/../kotori_results/$mol_name/"
if [ ! -d "$tgt_... |
8d86e269889564caa17a5fadc47ea39aeaaa7281ed245117eaa5a3754b1ba9cc | Shell | 6,862 | 152 | #!/bin/bash
python_path=/home/abnousa/software/python3.6.5/bin/python #should have pysam, pybedtools installed. bedtools, samtools should be in the path
Rscript_path=/opt/R-3.4.3/lib64/R/bin/Rscript
###################################################################
feather=1 #start from feather or run only MAPS
maps=1... |
ffae7dd892ca7d66ff2a23b65dc7b2e1cdcec881021e4a63e2aa8301699727da | Shell | 6,890 | 152 | #!/bin/bash
python_path=/home/abnousa/software/python3.6.5/bin/python #should have pysam, pybedtools installed. bedtools, samtools should be in the path
Rscript_path=/opt/R-3.5.0/bin/Rscript
###################################################################
feather=1 #start from feather or run only MAPS
maps=1
number_... |
19e4ea416ccb1957be1ca204188a640f7cca4a3ec226afd7fb8ed30db2bdf427 | Shell | 6,912 | 171 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL, Connectome Workbench (wb_command)
# environment: HCPPIPEDIR, FSLDIR, CARET7DIR
########################################## PIPELINE OVERVIEW ##########################################
# TODO
########################################## OUTPUT ... |
f31901ac17aea2bc49a48f5c410a3c18a16f37eb049cb2e648750c3343c14101 | Shell | 6,963 | 128 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Andreas Schuh
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Ap... |
0b68075b6577f1df4b4862a53b3c7c9b0f26835a6135f04f85e2eea6ae86399c | Shell | 6,964 | 125 | #!/bin/bash
PROJECT=/Volumes/Elements_CR/atrialmtk/src/3Processing/UAC_Codes
DATA="/Volumes/Elements_CR/atrialmtk/Examples/Example-Biatrial-MRI/3Processing"
ConvertFilesLoc=/Volumes/Elements_CR/atrialmtk/src/3Processing/UAC_Codes
PVLabelT=0.8
LAALabelT=0.35
UnitsRescale=1000
index=1
export PYTHONPATH=$PROJECT
ES_d... |
7223a16b95406548479ce2a789dcce311810172aa648d8b8c3b8f4bf0e38ab79 | Shell | 6,977 | 120 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/tempfiles.shlib" "$@"
opts... |
44d69c1b65a23a8e293890c2c4d13a5affc4d33aa204c65866da777337a98675 | Shell | 7,002 | 170 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
g_matlab_d... |
551fe77ebfb15545c7d3c0b3b0765648cb9a83876d5a618ffd19e3e965e2a3c7 | Shell | 7,080 | 152 | #!/bin/bash
python_path=/home/abnousa/software/python3.6.5/bin/python #should have pysam, pybedtools installed. bedtools, samtools should be in the path
Rscript_path=/opt/R-3.4.3/lib64/R/bin/Rscript
###################################################################
feather=1 #start from feather or run only MAPS
maps=1... |
a7f1d54549f938883cdea37ecd2e6098eaa8ea64244966af36c95138db48bbe7 | Shell | 7,084 | 140 | #!/bin/bash
# Usage: ./generic_registration.sh <structural_image> <structural_brain_flag> <reg_image> <reg_brain_flag> <target_image> <use_brain_flag> <direction_flag> [-m <mask_file>]
# 参数说明：
# structural_image: 结构像文件路径（如 T1）
# structural_brain_flag: 结构像是否已剥脑 (1 表示已剥脑，0 表示未剥脑)
# reg_image: 用于结构像配准的图像文件路径（如 fMRI 或 ma... |
3d28504b94e98d2de009a26915355fe97a264cbadf48805e3e58b6140b6de1b9 | Shell | 7,132 | 214 | #!/bin/bash
set -eu
# Example script to run fMRIStats pipeline on multiple subjects to compute
# fMRI quality metrics (mTSNR, fCNR, percent BOLD) after ICA+FIX cleanup
# Global default values
DEFAULT_STUDY_FOLDER="${HOME}/projects/HCPpipelines_ExampleData" # location of Subject folders (named by subjectID)
DEFAULT... |
117d485a21f9be966144eeee772c0fd9e61c7a712a671396d423d163b1f682ee | Shell | 7,138 | 182 | #!/bin/bash
source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@" # Debugging functions; also sources log.shlib
scriptName="basic_preproc_sequence.sh"
echo -e "\n START: ${scriptName}"
workingdir=$1
ro_time=$2 #in sec
PEdir=$3
b0dist=$4
b0maxbval=$5
echo "${scriptName}: Input Parameter: workingdir: ${workingdir}"
ec... |
5baea11d0b493001290380735e5d779c11895ea6f7124bd5bcc6e5164bc24bec | Shell | 7,151 | 32 | #!/usr/bin/env bash
set -euo pipefail
cd ..
device=0
surrogate=gaussian
surrogate=multi_gaussian
python online_main.py --model_type RLIF --nb_epochs 100 --method esd-rtrl --nb_hiddens 1024 --devices "$device" --normalization none --lr 0.01 --surrogate $surrogate --lr_step_size 5 --etrace_decay 0.93 --nb_layers 3 --s... |
80264e0231a74fcb0677c8c0c5e25e91b559ebacf03d89f8d0e627b79d2d1eac | Shell | 7,184 | 166 | #!/bin/bash
set -eu
# skeleton grabbed from ComputeGroupTICA.sh
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDI... |
987cd254eba252900a4827fa292711eaf439199c8934f34d4359e763efaa9e13 | Shell | 7,199 | 158 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
command_line_specified_study_folder=""
command_line_specified_subj=""
command_line_specified_run_local="FALSE"
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argument=... |
e81d200f4000d2ff4af6f38832d64548b1b7997677982795e4545280c56c9a53 | Shell | 7,204 | 207 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
#this function gets called by opts_ParseArguments when --help... |
cff425034495731eadbba00702b400d663293666f9a149e78df9a4de58f08cff | Shell | 7,220 | 144 | # train an ensemble of MPRAnn models
### script params/variables
ENSEMBLE_SIZE=10
OUTDIR=../results/MPRAnn
DATA_DIR=../data/lentiMPRA
CONFIG=../config/MPRAnn.yaml
PROJECT_NAME=MPRAnn_ensemble
DOWNSAMPLE_ARR=( 0.1 0.25 0.5 0.75 ) # used if downsample set to true
### define cell type
CELLTYPE='HepG2' # HepG2 or K562
OU... |
57fe191cb006b362813ceea81486c24987ab14a0c5b9b5e31acdbc9b23837dcd | Shell | 7,270 | 176 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
export HCPPIPEDIR="$(dirname -- "$0")/../.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/tempfiles.shlib" "$@"
opts... |
13afae8e5a705573cb4889eb1b17f62e305edc9dae478e514e330f95c5e7d42b | Shell | 7,276 | 181 | #!/usr/bin/env bash
# Generates a FreeSurfer group average subject from scratch (without fsaverage)
# Denis Chaimow 2024-01-24
set -Eeuo pipefail
script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P)
usage() {
cat <<EOF
Usage: $(basename "${BASH_SOURCE[0]}") -d <SUBJECTS_DIR> [Options]
Requir... |
695eedaedb3cc0a032db3b2fa97341ed49fcf2e6adce900429b17e7332d1ca0f | Shell | 7,356 | 195 | #!/bin/bash
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
script_name=$(basename "${0}")
show_usage() {
cat <<EOF
${script_name}: Sub-script of PostFreeSurferPipelin... |
3ad27864f6ac1c5f17b6d595c30e54a29abfe3b84caeac8c8f7c7f538fa21566 | Shell | 7,359 | 232 | #!/bin/bash
# ------------------------------------------------------------------------------
# Show usage information for this script
# ------------------------------------------------------------------------------
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
#fix this if... |
a948a04a44489ae32c4c438da578839795da06573407fee3d937cdabf43b1e82 | Shell | 7,388 | 251 | #!/bin/bash
# ------------------------------------------------------------------------------
# Usage Description Function
# ------------------------------------------------------------------------------
g_script_name=`basename ${0}`
show_usage() {
cat <<EOF
${g_script_name}: Generate Spin Echo Bias Field Prerequi... |
85c58967e3c08a648d41fea8ba6f531a02b906f3523ee433a9eb513b637edb7a | Shell | 7,446 | 169 | #!/bin/bash
command_line_specified_run_local=FALSE
while [ -n "$1" ]; do
case "$1" in
--runlocal) shift; command_line_specified_run_local=TRUE ;;
*) shift ;;
esac
done
#################################################################################################
# General input variables
#... |
a3cd6b40b0635c86551afacf52cf6b32d750c150f0094d6002cf2b2b4d903d51 | Shell | 7,456 | 293 | #!/usr/bin/env bash
set -e
# ============================================
# Native-space lesion filling using SynthMorph
#
# Final output:
# A single full-head lesion-filled T1 image at the path
# specified by -o (no separate brain-only output).
#
# Requirements:
# - FSL (fslreorient2std, fslswapdim, fslmaths)
#... |
13123a586d581e19f8ab948c3267082dede556185db86b265fa4a86df0b7b09b | Shell | 7,463 | 222 | #!/bin/bash
# Evaluation script for mcmlnet
# To capture the logging, run as: ./eval.sh | tee eval_$(date +%Y%m%d_%H%M%S).log
set -e
set -o pipefail
echo "=========================================="
echo "mcmlnet Evaluation Script"
echo "=========================================="
# Start timer
SCRIPT_START_TIME=$(d... |
3354c3ca047e99f12f9943831f89e5090fd74e7ac013ce569d0e1b88e0d5dc9e | Shell | 7,487 | 263 | #!/usr/bin/env bash
# 786
echo "Start: `date`"
GETOPT="getopt"
TIME="/usr/bin/time"
if [[ "$OSTYPE" == "linux-gnu" ]]; then
:
elif [[ "$OSTYPE" == "darwin"* ]]; then
GETOPT="$(brew --prefix gnu-getopt)/bin/getopt"
TIME="gtime"
else
echo "Unknown environment ${OSTYPE} --- use at your own risk!"
fi
$GETOPT --test... |
11c71b263b445d21b342ceeb88f79b88f94f4954dbb3c486868dcdc7fdeb9d39 | Shell | 7,491 | 258 | #!/bin/bash
#set -xv
# Naming assumptions
# This script assumes that:
# 1. The cross-sectional session dirs are named <Subject>_<PossibleVisit>,
# 2. Longitudinal session dirs are named <Subject>_<Possible_Visit>.long.<Template>,
# 3. Both longitudinal and cross-sectional sessions exist in the study folder.
# Globa... |
5a10c3b72385a73d0c98af840df5c16102445840ba5d45e1618939fbe168b559 | Shell | 7,631 | 147 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
#fix this if the script is more than one level below HCPPIPEDIR
export HCPPIPEDIR="$(dirname -- "$0")/.."
fi
source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$... |
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