sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
46d784c7ca9b62673be4b6b49410a18f24ac37329428d31bc1e0d6ec673b2b7c | Shell | 7,699 | 135 | #!/bin/bash
set -e
#Set of tests to run.
#
#List of tests:
#1) Train COMfinder on markerless mouse demo (two exp.yaml)
# Because tf 1.x struggles with random seed reproducibility,
# So it will be difficult to compare weight files directly.
# This is potentially solved by removing data shuffleing in
# a bespoke training... |
82114d95f6ae95b85a77985ec8c710712ad443aa6322454139e44d4a6634d44c | Shell | 7,701 | 168 | #!/bin/bash
# Description:
# This script generates the RGB-encoded Probabilistic Fiber Map (PFM)
# from brainstem-adjacent ROIs extracted from fs_preprocc_extract.sh
#
# Usage:
# ./trackgen/pfmgen.sh <INTERDIR> <LOGFILE> <OUTPUT_DIR> <THREADS>
#
# Positional args:
# 1. <INTERDIR> - Directory containing preproce... |
f261e4d10b1c66b3509c8212ca258c427e0a3cc8287901b34bc2f73627a8ef5d | Shell | 7,709 | 154 | #!/bin/bash
# script to align native surfaces with template space & resample native surfaces with template topology
# output: native giftis resampled with template topology
Usage() {
echo "align_to_template.sh <topdir> <subjid> <session> <age> <volumetric template> <surface template> <pre_rotation> <outdir> <con... |
3d464ba56b2b6d0fa6b2c63d17a06cb1bbf6d9a7ed880bece23e866d8ac020eb | Shell | 7,715 | 174 | #!/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 ${numArgs} ]; do
argument=... |
5871a9b09595b07c72c9877e18c3087701a3e442411fac19208bcd57476027b9 | Shell | 7,716 | 230 | #!/bin/bash
packages="ITK VTK MIRTK"
vars="dir install git branch version folder build cmake_flags make_flags"
usage()
{
base=$(basename "$0")
echo "usage: $base [options]
Setup of the DrawEM software.
Options:
-j <number> Number of CPU cores to be used for the setup (default: 1)
-build <d... |
fde692d105d718ce99a40dcebb15b9eece257369ed8b3d4f55f687b7df027938 | Shell | 7,824 | 236 | #!/bin/sh
#
# Test the various reports from meryl-lookup.
#
# Set 'meryl' to the path to the meryl executable. The script
# assumes 'meryl-lookup' can be found the same way.
#
# Set 'valgrind' to the empty string to run without valgrind.
#
length=31 # Manually verified!
length=393 # Longer!
meryl="/work... |
af71361507fe1576517854be48ccbed03ba6a8683fb85cfb414666d5b5421229 | Shell | 7,825 | 98 | #!/bin/bash
export PYTHONUNBUFFERED=1
# Step 1: make dataset
# python make_dataset.py --output-dir /home/ubuntu/simu_runs/run_B
# Step 2: run algorithms
# python -u run_destVI.py --input-dir /home/ubuntu/simu_runs/run_B --sc-epochs 15 --st-epochs 2500 --amortization latent
# python -u run_destVI.py --input-dir /home... |
c7833aed3d2c20ceab07ddfbfa8fc322d681fdf0231d541b770da6591d3407bf | Shell | 7,851 | 173 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
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 ${numArgs} ]; do
argument=... |
d8508f41e44790b2fae5445d0f9910a1fabe87865011b9217a0dba01f04bf721 | Shell | 7,853 | 157 | #!/bin/bash
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
script_name=$(basename "${0}")
show_usage() {
cat <<EOF
${script_name}: Sub-script of GenericfMRISurfacePro... |
ff6898e736d83d5c84ed91ffde49b9dc5df92fd958aade694fd9bd7bea6da5bc | Shell | 7,867 | 234 | #!/bin/bash
# Evaluation script for mcmlnet
# To capture the logging, run as: ./eval.sh | tee eval_$(date +%Y%m%d_%H%M%S).log
set -e
set -o pipefail
echo "=========================================="
echo "mcmlnet Evaluation Script"
echo "=========================================="
# Start timer
SCRIPT_START_TIME=$(d... |
0db24d950f50ec0112c66fab7f6bb3a17bbdad1f373806eccb5f3245e827d6d9 | Shell | 7,906 | 182 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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... |
fb1e71176b2209448680a90b218946b3f501af2d1679e5943d0e957bc2118e87 | Shell | 7,909 | 220 | #!/bin/bash
set -euo pipefail
########################################
# Usage
########################################
if [[ $# -lt 6 ]]; then
echo "Usage: $0 <bids_dir> <subject_id> <subregion_ha> <subregion_thalamus> <subregion_brainstem> <subregion_hypothalamus>"
echo " subregion_* should be 0 or 1"
echo "E... |
1550e98537e91737c35427485f78b43f774c532d35be7ab6d14ae0793cb9cccb | Shell | 7,947 | 219 | #!/usr/bin/env bash
set -euo pipefail
# Compare rb liftover vs paftools.js liftover coordinates
#
# KEY INSIGHT: paftools.js liftover takes query.bed and lifts to target space.
# rb liftover (default) takes target BED and lifts to query space.
# So we use rb --qbed to match paftools behavior: both take query coords, o... |
7851668c25f6da0261133854a7e576aac3d6d9eb6eeecb902fcd05b60ad695b0 | Shell | 7,969 | 215 | #!/bin/bash
# ChemGraph Kubernetes Deployment Script
# Deploys both Streamlit UI and MCP server
set -e
# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color
# Function to print colored messages
print_info() {
echo -e "${GREEN}[INFO]${NC} $1"
}
print_warn() {
ech... |
3c4dfed8aefbfbf9341ba61e1201100a4aa8994e1103f343fb81f3853a7ae723 | Shell | 7,999 | 172 | export SVN_REVISION=SVNREVNO
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/MCR/v80/bin/glnxa64:.
export MCR_DIRECTORY=/usr/local/MCR/v80
export INSTALL_PREFIX=`expr /usr/local/prototype_matlab/V"$SVN_REVISION"`
export DATASET_HOME=/home/anagendran/Desktop/Testing_environment/130913_cert_0542/
export DATASET_PREFI... |
fefbb648d8c2dbff25837cbbff99029377d227b46752d80a6d3a7cc4773e18f3 | Shell | 8,009 | 186 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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" "$@"
opts_Se... |
97ce4cde0f797dde6a79a7efc836361c1df934e2bc3ffe47abe4e5976a8fe43f | Shell | 8,216 | 213 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
command_line_specified_study_folder=""
command_line_specified_subj_list=""
command_line_specified_group_average_name=""
command_line_specified_reg_name=""
command_line_specified_symlink_study_folder=""
command_line_specified_run_loc... |
dbc5980cfafb45e704c580fca56b19def33afe450a1504f5cf074382f7eb6aaf | Shell | 8,225 | 186 | #!/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" "$@"
opts... |
b598f972f09dfd27b4c573de07d4752c099744c65d28d0311cf0e417bbbc4fac | Shell | 8,289 | 163 | #!/bin/bash
# SubcortSegmentNHP.sh
# The script edits subcortical segment (aseg) and white matter segment (wm) for NHP brain using FS6. The wm is deweighted
# for cortex and weighted for claustrum and white matter skeleton based on species template. Skeleton weighting is needed
# for NHP brain cortical surface anlaysis... |
0350418d2a9d78bd9a5b44476358c4a2b041fd5d2d766afae85d960eafe8178e | Shell | 8,300 | 221 | #!/bin/bash
DEFAULT_STUDY_FOLDER="${HOME}/data/7T_Testing"
DEFAULT_SUBJ_LIST="102311"
DEFAULT_RUN_LOCAL="FALSE"
DEFAULT_ENVIRONMENT_SCRIPT="${HOME}/projects/HCPpipelines/Examples/Scripts/SetUpHCPPipeline.sh"
SCAN_STRENGTH_CODE="7T"
DIRECTIONS="71 72"
#
# Function: get_batch_options
# Description:
# Retrieve the --... |
f1f9db672abc6d0b7d08e02c16b2f4e24748330f774d6d164c3bd0ef61af8e13 | Shell | 8,347 | 218 | #!/bin/bash
#SBATCH --time=336:00:00
### DEFAULT VALUES (MIGHT GET OVERRIDDEN BY USER CLI INPUT) ###
PIPELINE="rcpl.py"
RESOURCES="--plugin MultiProc --memory_gb 50 --n_procs 10"
MAX_JOBS=16
NICE=5
BRANCH='main'
SUBMIT_DELAY=72
CPUS_PER_TASK=15
CUSTOM_SETTINGS=""
#######################################################... |
c1a38a7f638e98560bb605335777931a42cf3c627ee562d08221f19680268704 | Shell | 8,384 | 234 | #!/usr/bin/env bash
set -euo pipefail
N_JOBS=12
usage() {
echo "Usage:"
echo " bash run_ARTS_fast_synthmorph.sh <subject> <age> <sex> <T1w_brain.nii.gz> <FLAIR_brain.nii.gz> <FA.nii.gz> <synthseg.nii.gz> <WMH_mask.nii.gz> <output_root>"
echo ""
echo "Example:"
echo " bash run_ARTS_fast_synthmorph.sh AFib0... |
dfe3ae5c1c52886dc8aa9edcddd30ac65033e93b779c334cf2cfdfdd74478847 | Shell | 8,470 | 159 | #!/bin/bash
ulimit -n 16000 && \
STAR \
--runThreadN 20 \
--soloType CB_UMI_Simple \
--soloCBwhitelist None \
--soloBarcodeReadLength 0 \
--soloFeatures GeneFull_Ex50pAS \
--soloCellFilter EmptyDrops_CR 10000 0.99 10 NULL NULL 500 0.01 20000 0.01 10000 \
--soloCellReadStats Standard \
--genomeDir /home/jonathan/STAR_g... |
60b3ed9120a6b155ac9fde4d93756d4a7521cd7a09f469a0320287b5bc5d2909 | Shell | 8,506 | 194 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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... |
05cbb60620f2198788ef51c63960f37114d59821f3512f81f48ed3f43732e5e6 | Shell | 8,525 | 186 | #!/bin/bash
# Start MCP and the planner/executor client inside an existing Aurora PBS allocation.
set -eo pipefail
abort() { echo "[ABORT] $*" >&2; exit 2; }
CG_INTERACTIVE=0
case "${1:-}" in
--interactive) CG_INTERACTIVE=1 ;;
"") ;;
-h|--help)
cat <<'USAGE'
Usage: bash examples/graspa_scaling/run.s... |
a2bd1a46ed83d03c70a354e53ec3c17c8dc21c02a288f4198e5aa849d9f5a1a5 | Shell | 8,572 | 459 | #!/bin/bash
declare -a s1
s1[1]=242
s1[2]=243
s1[3]=242
s1[4]=242
s1[5]=242
s1[6]=241
s1[7]=242
s1[8]=242
s1[9]=242
s1[10]=242
s1[11]=242
s1[12]=242
s1[13]=244
s1[14]=241
s1[15]=241
s1[16]=242
s1[17]=244
s1[18]=242
s1[19]=242
s1[20]=244
s1_nv[1]=188210176
s1_nv[2]=188987904
s1_nv[3]=188210176
s1_nv[4]=188210176
s1_nv[... |
3aa554eb84ecdcceb28fb17d7625fb5c13beb89e3912d94a91838c2d7e4778ba | Shell | 8,672 | 460 | #!/bin/bash
declare -a s1
s1[1]=242
s1[2]=243
s1[3]=242
s1[4]=242
s1[5]=242
s1[6]=241
s1[7]=242
s1[8]=242
s1[9]=242
s1[10]=242
s1[11]=242
s1[12]=242
s1[13]=244
s1[14]=241
s1[15]=241
s1[16]=242
s1[17]=244
s1[18]=242
s1[19]=242
s1[20]=244
s1_nv[1]=188210176
s1_nv[2]=188987904
s1_nv[3]=188210176
s1_nv[4]=188210176
s1_nv[... |
2b2b40c9c5e79f596f47e64414646286613085b39c6bb142a29dc9ac6ad6747e | Shell | 8,673 | 137 | #!/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"... |
de7a9767e3f0f4de1cd594c8608887e68aa00b740433f1cdb7aaf9ecc1256f2c | Shell | 8,712 | 205 | #!/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" "$@"
opts... |
35076b495182aa8f2ad34eca18c0a8888855a03c665a0293feb10def920b7555 | Shell | 8,807 | 304 | #!/bin/bash
export LC_ALL=C
Usage() {
echo ""
echo "Usage:"
echo " bedpostx_gpu_custom.sh --dwi <data.nii[.gz]> --bvec <bvecs> --bval <bvals> --mask <mask.nii[.gz]> --out-dir <output_dir> [options] [xfibres options...]"
echo ""
echo "Required:"
echo " --dwi Path to DWI image (4D)"
e... |
f73f1b5bf84daf83d7dbc3d8bff9babef7ca85b1ccc2d565c31bc7ee385a091b | Shell | 8,828 | 205 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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" "$... |
3df306712fdbcc66f6e079855613aaa2bba1f6e899dc68ef1f9f0e1ca95cd76f | Shell | 8,855 | 212 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
command_line_specified_study_folder=""
command_line_specified_run_local="FALSE"
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argument=${arguments[index]}
case "... |
ed1be86105ad3cfc9613a2a1393622b28e32c3755e654b1a88d4071b99cf367c | Shell | 9,035 | 152 | #!/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" "$@"
# ... |
15b08e8bddc61450c03b3baaef84bb85c3fccb4199b217151f0f1c89bbfbb007 | Shell | 9,041 | 275 | #!/bin/bash
################################################################################
# BCR Repertoire Processing Pipeline using Immcantation Suite
################################################################################
#
# Description: Process 10X Genomics single-cell BCR sequencing data using
# ... |
7aa6f4a8c257146a933449eb18c4d06380bafba901413332407fb0778e965d0b | Shell | 9,064 | 40 | CUDA_VISIBLE_DEVICES=0,6 python mf_hyper.py --device 1 --log_steps 1 --num_layers 3 --hidden_channels 128 --dropout 0.0 --batch_size 65536 --lr 0.0001 --epochs 1000 --eval_steps 10 --runs 1 --log_dir log_mf/run09 --n_par_combs 36 --curr_param_idx 0 &
CUDA_VISIBLE_DEVICES=6,0 python mf_hyper.py --device 1 --log_steps 1 ... |
6ab94beaa62ef6b9d9e546d06e930ed9b42832f424427beffbfb66cc0c7c5a42 | Shell | 9,080 | 185 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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"... |
5716d925672ccee396cf5c40a621b9cfdad429083da893b187e69a85e18347e6 | Shell | 9,143 | 181 | #!/bin/bash
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
script_name=$(basename "${0}")
show_usage() {
cat <<EOF
${script_name}
Usage: ${script_name} [options]
Us... |
821640e1446fe3224c557086734dffa32aebde006af34013b3d095ed467a5c0f | Shell | 9,167 | 191 | #! /bin/bash
# RescaleVolumeAndSurfaceNHP.sh
#set -eu
Usage_exit (){
echo "RescaleVolumeAndSurfaceNHP.sh <SubjectDIR> <SubjectID> <ScaleVolumeMatrix (world.mat)> <T1wImage> <T2wImage> <FLAIR|T2|NONE> [ScaleSuffix]"
echo
echo "Undo the NHP scaling of volumes for FreeSurfer, and also fix the scaling of surfaces, sulc, ... |
8c18981fd0f601b69fcff4796878724c2411c2e98e89d07e8d23462752549fde | Shell | 9,215 | 228 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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"... |
fcfc901303e58eb69f196cce95351d9854609706cc30523ba9c2cb9b678d2005 | Shell | 9,242 | 235 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL, FreeSurfer (version 5.3.0-HCP), Connectome Workbench (wb_command)
# environment: HCPPIPEDIR, FSLDIR, FREESURFER_HOME, CARET7DIR
########################################## PIPELINE OVERVIEW ##########################################
#TODO
... |
1d7a2c367903db6b8484637d63bf2e07071cc112b1ae4f9fc02e8f1f5ec4ad3b | Shell | 9,320 | 217 | #!/bin/bash
Usage () {
echo "$(basename $0) --StudyFolder=<path> --Subject=<id> --Species=<species> [options]"
echo ""
echo "Required Options:"
echo " --StudyFolder: Path to the study folder containing subject data"
echo " --Subject: Subject identifier (space-separated list allowed)"
echo " ... |
a351fef0b78cc21ca85ebd07cade65f64bedc45412d0806af3fef5148ff3fed1 | Shell | 9,324 | 125 | #!/bin/bash
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
script_name=$(basename "${0}")
show_usage() {
cat <<EOF
${script_name}: Sub-script of PostFreeSurferPipelin... |
ae6f6e8f11dbf00c363e4aa24ad3e9ef1b46f5eef78ad2bf82e9126019b70576 | Shell | 9,340 | 226 | #!/bin/bash
# Intensity normalisation, and bias field correction, and optional Jacobian modulation, applied to fMRI images (all inputs must be in fMRI space)
# This code is released to the public domain.
#
# Matt Glasser, Washington University in St Louis
# Mark Jenkinson, FMRIB Centre, University of Oxford
# 20... |
48a126f0a2602aa7a40e921e7ea19f156e9ccd28980d84acee5bb17995215a0b | Shell | 9,353 | 313 | #!/bin/bash
PRINT_USAGE () {
echo "Usage $0 [flags] [modules]" >&2;
echo "Valid modules: all, gui, simulator or batch (default is all)" >&2;
echo "Valid flags:" >&2;
echo "-f - force recompilation" >&2;
echo "-l - write build log on compile_commands.json" >&2;
echo "-q - quiet compilation. O... |
6e851bba806e4c0dd5fd722047ef508326b5b981cd346baa232cd53a68b23d22 | Shell | 9,382 | 179 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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" "$@"
opts... |
44ab88232c0d9bb92db4f4d82954b7949177454d29e1027b6a4a686eaa6d3769 | Shell | 9,448 | 40 | CUDA_VISIBLE_DEVICES=6,0 python node2vec_hyper.py --device 1 --log_steps 1 --embedding_dim 16 --walk_length 5 --context_size 5 --walks_per_node 5 --batch_size 128 --epochs 100 --lr 0.0001 --log_dir log_node2vec_fin2/run00 --n_par_combs 36 --curr_param_idx 0 &
CUDA_VISIBLE_DEVICES=0,6 python node2vec_hyper.py --device... |
7fd2049ddea8d5b2c6c9184cdfb9c2e7c439380c846509f53c7b6f4f40625380 | Shell | 9,449 | 230 | #!/bin/bash
#
# Run all figure making scripts.
#enviroment settings
set -e
set -o pipefail
# If RUN_LOCAL is used, the time-intensive steps are skipped because they cannot
# be run on a local computer -- the idea is that setting RUN_LOCAL=1 will allow for
# local testing running/testing of all the other figures
RUN_L... |
4a88ecdcf1fb50198dadb9a7cdc15778c63a7d84e35ddbe93f700e2aed4b2296 | Shell | 9,479 | 272 | #!/bin/bash
# Global default values
DEFAULT_STUDY_FOLDER="${HOME}/data/HCPpipelines_ExampleData"
DEFAULT_SUBJECT_LIST="100307 100610"
DEFAULT_ENVIRONMENT_SCRIPT="${HOME}/projects/HCPpipelines/Examples/Scripts/SetUpHCPPipeline.sh"
DEFAULT_RUN_LOCAL="FALSE"
#DEFAULT_FIXDIR="${HOME}/tools/fix1.06" ##OPTIONAL: If not set... |
401343be8fbe84b69da998d2d56ffea64ad1ebae29370a8333ee7ab128f65073 | Shell | 9,665 | 230 | #!/bin/bash
# Description:
# This script extracts the mean low-b from the input DWI and performed SynthSeg
# and brainstem-subregion ROI extraction for tractography seeding.
#
# Usage:
# ./freesurfer_preprocess.sh <input_dir>
#
# Positional args:
# 1. <input_dir> - Directory containing `input_dwi.nii.gz` (requir... |
280654a8055460ad635bf782bf512fabf4df49f99a51a41cae3c83d1e0717012 | Shell | 9,807 | 250 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
# code for transforms adapted fro... |
d01ad6f910ad8abbeca505e6186350b93e2a5e05a4ab2eb810ebae14756c2293 | Shell | 9,923 | 234 | #from Jun, tweaked by Beth
#!/bin/bash
# Define the location of the script path
script_path="/net/shendure/vol1/home/martin91/scripts/sciRNAseq3"
################################################################################
###Experiment-specific settings
# define the fastq folder including all fastq files
fas... |
6461b66c0575a4bd1e893ce1893a29ba0e2f107f3e7ccf7b29e0f385f1cc0cc7 | Shell | 10,110 | 362 | #!/usr/bin/env bash
set -e
# ======================================================
# Symmetric-MNI-based contralateral mask generation (SynthMorph)
#
# Modes:
# Default mode:
# - Generates filled T1 in native space and JSON sidecar (as original)
# Contra-only mode (--contra-only):
# - Generates only contr... |
779f51221b2c02e36409683257a37dc39cbfd5a4834a496ea3e2f8d2f8d833ad | Shell | 10,180 | 201 | #!/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" "$@"
opts_SetScriptDescription "run only the individual parts of tran... |
6251f2951051e3095e7c0eb35267e3b6873e3b7beda81d52995ee530734e6314 | Shell | 10,225 | 297 | #!/bin/bash
set -e -E -u -o pipefail
# defaults
ARCH=$(uname -m)
# set up R environment
export CRAN_MIRROR="https://cran.rstudio.com"
export R_LIB_PATH=~/Rlib
mkdir -p $R_LIB_PATH
export R_LIBS=$R_LIB_PATH
export PATH="$R_LIB_PATH/R/bin:$PATH"
# reference for configuring 'R CMD check' via environment variables:
# h... |
957d3440d11b5c00041caf4a2f513d92f5f61bd1256a056be74a8ea6ffdc18f7 | Shell | 10,231 | 371 | #!/usr/bin/env bash
set -euo pipefail
APP_NAME="inference_app"
AUTH_CLIENT_ID="58fdd3bc-e1c3-4ce5-80ea-8d6b87cfb944"
GATEWAY_CLIENT_ID="681c10cc-f684-4540-bcd7-0b4df3bc26ef"
GATEWAY_SCOPE="https://auth.globus.org/scopes/${GATEWAY_CLIENT_ID}/action_all"
SESSION_REQUIRED_POLICY="83732ff2-9c42-4548-b5ce-17e498c84f6a"
AU... |
fcbafcb76531f34614b26b9493b1d8e7e0c5205b4f3b4f5e041ddd263e1b5d01 | Shell | 10,313 | 229 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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" "$@"
opts... |
507f92213ccf4834bd9be8d3a60ad9097099aa54622be05f1cf028a01eb844a9 | Shell | 10,476 | 234 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL>=6.0.6 (including python with numpy, needed to run aff2rigid - part of FSL)
# environment: HCPPIPEDIR, FSLDIR
# ------------------------------------------------------------------------------
# Usage Description Function
# --------------------... |
767a993a4f430ac75612e61c12ee52cba9345e9e126253184dff3efa2a0c3fdd | Shell | 10,481 | 282 | # ALPS
# REQUIRED INPUTS:
fa_img='' # Input FA image (NIfTI format): -fa_img <path>
output_dir='' # Output directory: -output_dir <path>
alps_dir='' # ALPS script directory: -alps_dir <path>
register_method='flirt' # Registration method: flirt or synthmorph: -register_method <method>
# OPTIONAL INPUTS:
xx_img='' # In... |
c1ef1dbda3ff9ca4fab77b3437b536cbecbd24b18fbc898315d6437ab6241848 | Shell | 10,563 | 208 | #!/bin/bash
set -eu
source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
source "$HCPPIPEDIR/global/scripts/tempfiles.shlib" "$@"
StudyFolder="${1}"
Subject="${2}"
fMRIName="${3}"
CorticalLUT="${4}"
SubCorticalLUT="${5}"
Caret7_Command="${6}"
LowResMesh="${7}"
RegNames="${8}"
SmoothingFWHM="${9}"
FinalfMRIResolution=... |
ca4a8935e128c03a76b652fd58aac5d7bf680ccc0445a4095bd91ab9d1423eda | Shell | 10,732 | 161 | #!/bin/bash
# # 2024-04-11
# # convert mgh
# cur_path=/Users/bo/Documents/data_liujia_lab/analysis_liuP1_greeble/MRI_results_FFT/new_stat_fft_subj
# mri_vol2surf --mov $cur_path/Corr_bin10_g123_freq6_ws0_clustere_corrp_tstat1_binary_wr_c30r.nii.gz --surf white --reg /Applications/freesurfer/7.3.2/subjects/register_2... |
2d5375374c7715e03a8b5f94f0f425a74b2c93a073a4bdf339e6f0dde5afd0fa | Shell | 10,785 | 315 | #!/bin/bash -
#
# File: git-archive-all.sh
#
# Description: A utility script that builds an archive file(s) of all
# git repositories and submodules in the current path.
# Useful for creating a single tarfile of a git super-
# project that contains other submodules.
#
# Exa... |
abed94264fa3c9f8ecf416966e782bad6e316c6d8e119cbade7cab38480d504d | Shell | 10,966 | 253 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # DiffPreprocPipeline_Eddy.sh
#
# ## Copyright Notice
#
# Copyright (C) 2012-2016 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Stamatios Sotiropoulos, FMRIB Analysis Group,... |
3ffe1ac21598166fbcf5b667f54e8f03855a5587986abdfae3a7cb8038b043cc | Shell | 11,063 | 263 | #!/usr/bin/env bash
set -euo pipefail
# Absolute path to this bash script
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PY_EXTEND="${SCRIPT_DIR}/../../../utils/python/extend_mask_x.py"
if [[ ! -f "$PY_EXTEND" ]]; then
echo "[ERROR] extend_mask_x.py not found: $PY_EXTEND"
exit 1
fi
if [[ $# -lt 7 ]];... |
8ce04d471b97bad1bdfafe88f9889dccc4fac01e4134b4787202a786873303d3 | Shell | 11,088 | 280 | #!/bin/bash
DEFAULT_STUDY_FOLDER="${HOME}/data/7T_Testing"
DEFAULT_SUBJ_LIST="132118"
DEFAULT_RUN_LOCAL="FALSE"
DEFAULT_ENVIRONMENT_SCRIPT="${HOME}/projects/HCPpipelines/Examples/Scripts/SetUpHCPPipeline.sh"
#
# Function: get_batch_options
# Description:
# Retrieve the --StudyFolder=, --Subjlist=, --EnvironmentScr... |
313d687803a93e6e852686b192414b0710c8cda904911ef5d55da59fb2c3d635 | Shell | 11,098 | 234 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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... |
150b28f0602935d4b21bcec44fa0693b375d9e900d62a3ced44692d341ed9927 | Shell | 11,241 | 257 | #!/bin/bash
set -eu
# Requirements for this script
# installed versions of: FSL
# environment: HCPPIPEDIR, FSLDIR
########################################## PIPELINE OVERVIEW ##########################################
#TODO
########################################## OUTPUT DIRECTORIES ############################... |
791a1bd8ca91b3fd987d6f5fa0e28e344cc249ebaa4e4a953f3d3477b592a9e6 | Shell | 11,394 | 302 | #!/bin/bash
set -eu
# this is an example script to run the tICA pipeline to clean a batch of subjects with group sICA and group tICA results that are both generated from a previous computation
# steps that aren't needed for this mode are automaticaly skipped inside the pipeline
# please make sure that precomputed gro... |
1c71394577a14ee04ec64e06397e45a6c975e4a9099e653e2643663d54123fe0 | Shell | 11,412 | 258 | #!/bin/bash
set -eu
# this is an example script to run the tICA pipeline to clean a batch of subjects with group sICA and group tICA results that are both generated from a previous computation
# steps that aren't needed for this mode are automaticaly skipped inside the pipeline
# please make sure that precomputed gro... |
b9cf06aee63527c2e966d6ced10225ff2d7ee85941a12a0c7d49eea3e8f6725b | Shell | 11,470 | 106 | #!/bin/bash
# var_array_1=(fe fe fe)
# var_array_2=(1 2 3)
# auto_cost_pyfile=(main_mpi_nc3 main_mpi_nc3_other main_mpi_nc3_no_auto_cost)
# auto_cost_pyfile=(main_mpi_nc3)
auto_cost_pyfile=(main_mpi)
arch_array=(
fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe f... |
97d7df4e059eb212070a6ef0d278885fdd5709b7ea8dd753f0803deca09de4fa | Shell | 11,736 | 301 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # DiffPreprocPipeline_PostEddy.sh
#
# ## Copyright Notice
#
# Copyright (C) 2012-2016 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Stamatios Sotiropoulos, FMRIB Analysis Gr... |
028c5fd2b857c3ece4ed6053dc12ce8805e21d8cacff045ccc5c7278c6a441e0 | Shell | 11,738 | 280 | #!/bin/sh
#
# Before building a release:
#
# Make a place to work, grab the bits you want to release:
# git clone git@github.com:marbl/PACKAGE PACKAGE-release
# cd PACKAGE-release
#
# Commit to master:
# Increase version in documentation/source/conf.py (if present)
# Increase version in src/main.mk
#
# ... |
13799f805ecfc5696eab22f952bafd8ceaafad2e5fd43a9efce43890ca8c65b8 | Shell | 11,761 | 204 | #!/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/parallel.shlib" "$@"
opts_Set... |
c8be38cf520b68103bba99812b722a51190acb8135b03a2d067d34af3ec8c8ef | Shell | 11,792 | 257 | #! /bin/bash
# Takuya Hayashi, RIKEN Brain Connectomics Imaging Laboratory, Kobe
# Tim Coalson, Washington University in St. Louis
set -eu
pipedirguessed=0
if [[ "${HCPPIPEDIR:-}" == "" ]]
then
pipedirguessed=1
#fix this if the script is more than one level below HCPPIPEDIR
export HCPPIPEDIR="$(dirname -... |
0199e3e4b27049acddff885f91744bdb3bd64023fee1b8122f64af37db406f7a | Shell | 11,880 | 111 | #!/bin/bash
# var_array_1=(fe fe fe)
# var_array_2=(1 2 3)
# auto_cost_pyfile=(main_mpi_nc3 main_mpi_nc3_other main_mpi_nc3_no_auto_cost)
# auto_cost_pyfile=(main_mpi_nc3)
auto_cost_pyfile=(main_mpi)
arch_array=(
fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe f... |
a2d5f0ae859f3f3b333f94450959fe966988bdda42069f66089c92bb2301ea12 | Shell | 11,936 | 202 | #!/bin/bash
# script to align native surfaces with template space & resample native surfaces with template topology
# output: native giftis resampled with template topology
Usage() {
echo "align_to_template.sh <topdir> <subjid> <session> <age> <volumetric template> <surface template> <pre_rotation> <outdir> <con... |
33ec061ed10cb8dd60d2dff482810d800f5bd3fda7576e856444221e8c4f39cf | Shell | 11,955 | 214 | #!/bin/bash
source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@" # Debugging functions; also sources log.shlib
echo -e "\n START: eddy_postproc"
#Hard-Coded filename. Flag from eddy to indicate that the jac method has been used for resampling
EddyJacFlag="JacobianResampling"
workingdir=$1
GdCoeffs=$2 #Coeffi... |
ae3ff3159ea9a58f56d1465ef9dc8fa682d3fbdfbe0c83a9af6c61321d976f22 | Shell | 12,090 | 203 | #!/bin/bash
# script to align native surfaces with template space & resample native surfaces with template topology
# output: native giftis resampled with template topology
Usage() {
echo "align_to_template.sh <topdir> <subjid> <session> <age> <volumetric template> <surface template> <pre_rotation> <outdir> <con... |
b6722838df42d9c48839f8fb5fefc1e05cdbdd4721d8923e0d9ffc534b66aa7a | Shell | 12,449 | 287 | #!/bin/tcsh -xef
# You can specify multiple monkeys and session, if performing preprocessing on multiple
# Files at once. Here, example for 5 sessions
set monkey = (your_monkey)
set session = (s1 s2 s3 s4 s5)
set bp_l = (.1)
set bp_h = (.01)
set resolution = Low_Resolution #resolution of the final maps
###### Define ... |
06b5e4ca56ff1d3200c36488f1ab2a74459303e2b4954d3cf7fc458b32c401d0 | Shell | 12,858 | 309 | #!/bin/bash
StudyFolder="<MyStudyFolder>"
#The list of subject labels, space separated
Subjects=(HCA6002236)
PossibleVisits=(V1_MR V2_MR V3_MR)
ExcludeVisits=()
Templates=(HCA6002236_V1_V2_V3)
EnvironmentScript="<hcp-pipelines-folder>/scripts/SetUpHCPPipeline.sh" #Pipeline environment script
# Requirements for this... |
9627d5694b211eb4fc1fd6e377611f4a77d35738ee9083dc18247d5b52f04599 | Shell | 12,916 | 109 | #!/bin/bash
# var_array_1=(fe fe fe)
# var_array_2=(1 2 3)
# auto_cost_pyfile=(main_mpi_nc3 main_mpi_nc3_other main_mpi_nc3_no_auto_cost)
# auto_cost_pyfile=(main_mpi_nc3)
auto_cost_pyfile=(main_mpi)
arch_array=(
fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe fe f... |
d5b3341d9a773a3dd6366d1ad52286102fbf1e773aacc56c0cba66457a329482 | Shell | 12,916 | 581 | #!/bin/bash
set -e
WARN='\033[0;31m'
INFO='\033[0;34m'
ERROR='\033[0;31m'
NC='\033[0m' # No Color
#MAIN BUILD VARIABLES
C_COMPILER="gcc"
CXX_COMPILER="g++"
AR_COMMAND="ar"
RANLIB="ranlib"
C_FLAGS=
ROOT_DIR=$(pwd)
BUILD_TYPE="release"
RUNTIME_OUTPUT_DIRECTORY=$ROOT_DIR
LIBRARY_OUTPUT_DIRECTORY=$ROOT_DIR
GLOBAL_FORCE... |
3d00ae3b081c5a571e144088b03c52e4f4a7b094bdfcb4ec97ee24bbb872bbb1 | Shell | 12,920 | 291 | #!/usr/bin/env bash
set -eu
function usage() { cat << EOF
run.sh: submits the master job of pipeline to the job scheduler.
USAGE:
run.sh <MODE> [-h] [-c CACHE] \\
-o OUTDIR \\
-j MASTER_JOB_NAME \\
-b SINGULARITY_BIND_PATHS \\
-t TMP_DIR
SYNOPSIS:
This script creates/submits... |
56d2ddfc0d9ae4f36c034435becca76b303ce2d14fb314d7d8df952c64f45666 | Shell | 12,925 | 292 | #!/bin/bash
set -eu
# this is an example script to run the full tICA pipeline with new estimations on both group sICA and group tICA
# since the step ClassifyTICA is not integrated yet, manual classification must be done (the pipeline will stop and give a message about manual classification)
# then please rerun the p... |
775f5604a4f71518d4b5b545f99a64f1f9504359251f8be14daca3a5b1e80982 | Shell | 12,933 | 266 | #!/bin/bash
# # PostFreeSurferPipelineLongLauncher.sh
#
# ## Copyright Notice
#
# Copyright (C) 2022-2024 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Mikhail Milchenko, Department of Radiology, Washington University in S... |
4495220c3c34f11e3495355d903aab7e27957ca746b95e661080378242c7fe8a | Shell | 12,947 | 250 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL>=6.0.6
# environment: HCPPIPEDIR, FSLDIR, HCPPIPEDIR_Templates
# ------------------------------------------------------------------------------
# Usage Description Function
# -------------------------------------------------------------------... |
bb97896f47d508255f56f8e84beae81a9b8cc46502da7b23aa4fb7b74988680d | Shell | 13,068 | 273 | #!/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" "$@"
opts... |
655c4273cca0766111ee990ba874afcc03f4bfd957bc02a5c5c0dfc21a32aa47 | Shell | 13,116 | 153 | #!/bin/bash
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
script_name=$(basename "${0}")
show_usage() {
cat <<EOF
${script_name}: Sub-script of GenericfMRISurfacePr... |
f85075166fdc91c56bc3c059e202bb62b3c68a779f87ba8293ff0341b4a88b21 | Shell | 13,199 | 404 | #!/usr/bin/env bash
# Generate dummy test data for Snakefile dry-run testing in CI
set -euo pipefail
BASE="$(cd "${GITHUB_WORKSPACE:-.}" && pwd)/tests/testdata"
rm -rf "$BASE"
###############################################################################
# Shared resources
##########################################... |
761a7507c4e8db695bb3edf42aca202f2a4df3c6ebb93529bcb1c3219038cbec | Shell | 13,428 | 353 | #!/bin/bash
set -e -E -o -u pipefail
# defaults
CONDA_ENV="test-env"
IN_UBUNTU_BASE_CONTAINER=${IN_UBUNTU_BASE_CONTAINER:-"false"}
METHOD=${METHOD:-""}
PRODUCES_ARTIFACTS=${PRODUCES_ARTIFACTS:-"false"}
SANITIZERS=${SANITIZERS:-""}
ARCH=$(uname -m)
LGB_VER=$(head -n 1 "${BUILD_DIRECTORY}/VERSION.txt")
# create the ... |
b4450ee8d93e2d6b8313e960ed4db64d6ab6e21cd4c891dd42e91991dc2c80d9 | Shell | 13,703 | 282 | #!/bin/bash
source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@" # Debugging functions; also sources log.shlib
scriptName="basic_preproc_best_b0.sh"
echo -e "\n START: ${scriptName}"
workingdir=$1
ro_time=$2 #in sec
PEdir=$3
b0maxbval=$4
echo "${scriptName}: Input Parameter: workingdir: ${workingdir}"
echo "${scrip... |
36f789664a7e0809d16d108f92f5a4aed5bd23d0b76e8e84c71664356ffe55a9 | Shell | 13,808 | 316 | #!/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 ${numArgs} ]; do
argument=... |
9cfbee05ee7e1eef125de6826e7381d5a9039aeee36d86022b797402c2282bdf | Shell | 13,900 | 204 | #!/usr/bin/env bash
wnids=(
n01440764 n01443537 n01484850 n01491361 n01494475 n01496331 n01498041 n01514668 n01514859 n01518878 n01530575
n01531178 n01532829 n01534433 n01537544 n01558993 n01560419 n01580077 n01582220 n01592084 n01601694 n01608432
n01614925 n01616318 n01622779 n01629819 n01630670 n01631663... |
60e059db5ae7a741a3a91a356758e2f8a3c881a1778af6fc4910259f07f3727b | Shell | 13,952 | 60 | CUDA_VISIBLE_DEVICES=5,7 python gnn_hyper.py --device 1 --log_steps 1 --num_layers 2 --hidden_channels 128 --dropout 0.0 --batch_size 65536 --lr 0.0001 --epochs 1000 --eval_steps 10 --runs 1 --log_dir log_gnn_gcn/run06 --n_par_combs 54 --curr_param_idx 0 &
CUDA_VISIBLE_DEVICES=7,5 python gnn_hyper.py --device 1 --log... |
791534b810f7026ff972d06c406121df37c0eb907c16ca5af26d2c0e9731815d | Shell | 14,011 | 325 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL
# environment: HCPPIPEDIR, FSLDIR, HCPPIPEDIR_Global
# --------------------------------------------------------------------------------
# Usage Description Function
# ---------------------------------------------------------------------------... |
2e23136e59a5a1fc4580cfb846a2e058da15afb773c4e686f93c2770648e7f9c | Shell | 14,099 | 378 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # LongitudinalFreeSurferPipeline.sh
#
# ## Copyright Notice
#
# Copyright (C) 2015-2024 The Human Connectome Project/Connectome Coordination Facility
#
# * Washington University in St. Louis
# * Univeristy of Ljubljana
#
# ## Author(s)
#
# * Jure Demsar, Faculty of Com... |
6fb5d0e1555eebc3ce31e10a17658b66a96cc7d11ff2893352069977e0b63f63 | Shell | 14,146 | 209 | #!/bin/bash
source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@" # Debugging functions; also sources log.shlib
echo -e "\n START: DiffusionToStructural"
########################################## SUPPORT FUNCTIONS ##########################################
# function for parsing options
getopt1() {
sopt="$1"
shi... |
f272086d7a1fde17343d4b69d8e9020cf4070051e298c7c50efe071362b3f2c0 | Shell | 14,315 | 306 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL, gradunwarp (HCP version)
# environment: HCPPIPEDIR, FSLDIR, HCPPIPEDIR_Global, PATH for gradient_unwarp.py
# -----------------------------------------------------------------------------------
# Constants for specification of Averaging and R... |
a9f057e8cd7997478c7e9d32be8104d98bbc15f93de6867187a9ee3dbc514b18 | Shell | 14,349 | 479 | # #!/bin/bash
# set -e
# # Initialize default values
# RUN_FASTSURFER=false
# DILATE=0
# SCRIPT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
# VERSION="$(grep "^version\\s*=\\s*\"" "$(dirname "${BASH_SOURCE[0]}")/pyproject.toml")"
# VERSION="${VERSION/version = /}"
# VERSION="${VERSION//\"/}"... |
b9835c4a19b042b64db8e27298953b8cec6f8c4d956230a5d3cb1bd26a93ce12 | Shell | 14,375 | 331 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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" "$@"
sourc... |
088028d789305aa819fb535f866b4855da26cf7f0c68b866717ebcdeb0474183 | Shell | 14,385 | 303 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # TaskfMRIAnalysis.sh
#
# ## Copyright (C) 2015 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# # Oxford University
#
# ## Author(s)
#
# * Timothy B. Brown, Neuroinformatics Research Group, Washington University in St.... |
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