sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
52951b1d402bda54589cc1e1334db4681b6ea2ed86e9329e355bd55f309303d9 | Shell | 3,852 | 54 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/SingleEcho/FIX/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
#NATIVE SPACE MAPS ONLY
wm_probability_m... |
95e63c4318c942de4bbfc53b6390c3b4cbd60ae00d153099c5359cfa6ad77ae8 | Shell | 3,863 | 56 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/SingleEcho/NO_AROMA/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
#NATIVE SPACE MAPS ON... |
4ffb98c253b766d9ad9305ffa97858328856f2eed54c6954686632fd0f381861 | Shell | 3,894 | 54 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/SingleEcho/AROMA/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
#NATIVE SPACE MAPS ONLY
wm_probability... |
672b94b221d3774c1aa770dc90741c69682ca6f8f88472f1dedd8c0a478eb7a6 | Shell | 3,937 | 140 | #!/bin/bash
echo
echo '****************************************'
echo '*** NeuroMiner ***'
echo '*** SGE joblist manager: ***'
echo '*** Train and crossvalidate models ***'
echo '*** (c) 2022 N. Koutsouleris ***'
echo '****************************************'
echo ' ... |
d49690f38fdbbd38a78a1a2ddaac0f5e1f5d96f515b39de7e1bafa94ec24c9ca | Shell | 4,011 | 144 | #!/bin/bash
echo
echo '****************************************'
echo '*** NeuroMiner ***'
echo '*** SGE joblist manager: ***'
echo '*** Simulate data and train models ***'
echo '*** (c) 2022 N. Koutsouleris ***'
echo '****************************************'
echo ' ... |
dd445ae4ce27e691d183368ac57feed7fb227adbddc53d71b743c6bbce39bcb3 | Shell | 4,027 | 115 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
a23d96c3ff728fa79a16c402a3c6ad97d631c0a4fa9a2e655856542cc0a13216 | Shell | 4,033 | 116 | #!/bin/bash
# This wrapper script is for running CUDA jobs (hint hint, OpenMM) on clusters.
# Load my environment variables. :)
. ~/.bashrc
# Make sure the Cuda environment is turned on
# module load cuda
# module load cudatoolkit
# export OPENMM_CUDA_COMPILER=`which nvcc`
# export BAK=$HOME/temp/runcuda-backups
if... |
4e6ca81e1c74e3eda884f4ddc48370d74bc2025752c0d7cb813fabc6879a68ee | Shell | 4,118 | 114 | Subject_name=$1
Root=$2
T1=$3
for file in "$Root"/*
do
result=$(echo $file | grep "fLoc")
if [ "$result" != "" ]; then
for t in "$file"/*
do
echo $t
echo "###########################"
lines=$(find $t -name "*SURF*" | wc -l)
if [ $lines -eq 0 ]; then
PhaseAP=$(find $t -name ... |
c2b18d06526be71bfb19059392580b809502e14989ea8f7060ee12d75ddb28e6 | Shell | 4,187 | 62 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/ME-ICA/NO_AROMA_or_FIX/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
#NAT... |
c03a9be0befd6525aa13b2975b4f5c5d0e6a60f3d97012fbd3a857dd920094e5 | Shell | 4,276 | 114 | #!/bin/bash
#=======================================#
#| Step 1 : Before downloading package |#
#=======================================#
#----
# Provide install prefix for cctools as well as
# locations of Swig and Python packages (i.e. the
# executable itself is inside the bin subdirectory).
#
# This is to ensure t... |
b0ed874de534d6e5c8935c3654607af82ac59044d83bdc645192c2566e350320 | Shell | 4,315 | 136 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
5afaff4f74503efc2ff1b2a9d4e5a95163bcbd779490ff51546daf667be2be37 | Shell | 4,347 | 112 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
source ${TOOL_BASH_LIB}
set -o pipefail
set -xuv
# Get Parameters
CHR_PREFIX=${CHR_PREFIX-}
CHR_SUFFIX=${CHR_SUFFIX-}
FILENAME... |
6b8aeff570768769c079b7513ababf8d2ccea5524c1db96a21540bf7488817a7 | Shell | 4,487 | 117 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
source $TOOL_BASH_LIB
set -xuv
bamfile=${FILENAME_MERGED_BAM}
# Get atomic filename of bam_file
bamfile_basename=`basename ${b... |
72eb4185212569dc21e7fa774112515a004149e917a98f39fe2d3e18ea3a2e58 | Shell | 4,529 | 111 | #!/bin/env bash
#SBATCH --job-name=Freesurfer
#SBATCH --account=kg98
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G
#SBATCH --time=30:00:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
#SBATCH --array=1-X
# A... |
d95313e15095fe39e441c431f0f067b1d95628bf03e9718fe5aa1927c0df1076 | Shell | 4,535 | 118 | #!/bin/bash
# Check if all arguments are provided
if [ "$#" -ne 2 ]; then
echo "Usage: $0 <ARG1> <ARG2>"
exit 1
fi
ARG1=$1
ARG2=$2
# Set the session name
SESSION_NAME=${ARG1}
# Start tmux session if it doesn't already exist
tmux has-session -t $SESSION_NAME 2>/dev/null
if [ $? != 0 ]; then
tmux new-sess... |
a57362228089e41e9d34b9ab073fda0b8b04b47581d61acab77bfa6c2ba65cc0 | Shell | 4,693 | 118 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# Reads methylation calls from methylCtools and writes to stdout
input_filename=$1
context=$2 # Either 'CG' or 'CH'
# Convert me... |
0ab1e2144af6ade7b849cecdfb13d4429eaaa8d731a0ea6e8bcffdcdd06eb70f | Shell | 4,704 | 165 | #!/bin/bash
echo
echo '****************************************'
echo '*** NeuroMiner ***'
echo '*** SGE joblist manager: ***'
echo '*** Interpret model predictions ***'
echo '*** (c) 2022 N. Koutsouleris ***'
echo '****************************************'
echo ' ... |
a57f310d3bf8e1340db03ecc3d12405dde22b04cc0d1547763fe7b8031a6f17a | Shell | 4,822 | 214 | #!/bin/bash
# Bash shell script to register BIDS data to the T1w
#
# Requires ants
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 20/02/2022
version="0.1"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir is made in main_functions
# FUNCTIO... |
8b56e0ba5aa1ef03f48077333da8e6017756db996a1b05657b81bcb623bf1ebf | Shell | 4,875 | 169 | #!/bin/bash
echo
echo '****************************************'
echo '*** NeuroMiner ***'
echo '*** SGE joblist manager: ***'
echo '*** Apply models to independent data ***'
echo '*** (c) 2022 N. Koutsouleris ***'
echo '****************************************'
echo ' ... |
283f45cce387975788a626cb91608046938348e710d1de3b0c6734423f8c6fa5 | Shell | 4,877 | 169 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
99a54d929124cc4c35773deaa43700a4b7193fd45f7ecef1a8a468ff15f437b1 | Shell | 4,883 | 166 | #!/usr/bin/env bash
# ============================================================
# make_bulk_vcf.sh — FINAL HARDENED VERSION
# ------------------------------------------------------------
# Merge multiple per-donor VCFs into a single bulk VCF,
# filter by MAC and F_MISSING, index the VCF,
# and output a summary.
#
# ... |
a8f9ff6d926c5967d68bc613eece2e4341b17c7f746e0538e670e221dd320add | Shell | 4,993 | 64 | python main.py 0.01 0.211 0.633 0.012 0.000844 0.0001 0.002 11.562640190124512 8
python main.py 0.05 0.211 0.633 0.012 0.000844 0.0001 0.002 11.562640190124512 8
python main.py 0.1 0.211 0.633 0.012 0.000844 0.0001 0.002 11.562640190124512 8
python main.py 0.4 0.211 0.633 0.012 0.000844 0.0001 0.002 11.562640190124512 ... |
6c41f0b3849d40183655f12f7d9de860e33d71d6f2ce5878e9e4c62dea9bcfe1 | Shell | 5,082 | 173 | #!/bin/bash
echo
echo '****************************************'
echo '*** NeuroMiner ***'
echo '*** SGE joblist manager: ***'
echo '*** Visualize models ***'
echo '*** (c) 2021 N. Koutsouleris ***'
echo '****************************************'
echo ' ... |
1c57fadfb46c56980d919ecd8b259862183c8e5ac2cd7f5bb0ce9396f7b2dad7 | Shell | 5,091 | 276 |
model_name=SCINet
python3 -u run.py \
--task_name long_term_forecast \
--is_training 1 \
--root_path ./dataset/TY/ \
--data_path TY2015.csv \
--model_id ETTh1_96_96 \
--model $model_name \
--data custom \
--features S \
--seq_len 96 \
--label_len 48 \
--pred_len 48 \
--e_layers 1 \
--factor... |
1d711476633c18c80cb64fdb459b754df8f62eeb27d9c2105d2294658222c0d5 | Shell | 5,128 | 276 |
model_name=TimeXer
python3 -u run.py \
--task_name long_term_forecast \
--is_training 1 \
--root_path ./dataset/TY/ \
--data_path TY2015.csv \
--model_id ETTh1_96_96 \
--model $model_name \
--data custom \
--features M \
--seq_len 96 \
--label_len 48 \
--pred_len 48 \
--e_layers 1 \
--facto... |
cf06704e4d18152a1ef0f2ce2d59da7b3346633613528b21bea2680724edffcd | Shell | 5,133 | 193 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
75dc7ffbfdd5c50cfcf00857a5535f80ad9fa8798ba2604f2ef5f04070a298da | Shell | 5,163 | 160 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
6ac869362be3019c79cf1e61774c6e2864a430b890dbe50f64e6507546263a91 | Shell | 5,205 | 248 | #!/bin/bash
# Bash shell script to prepare fMRI/DTI results for Brainlab Elements Server
#
# Requires Mrtrix3, Karawun
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 07/12/2020
version="0.1"
kul_main_dir=`dirname "$0"`
source $kul_main_dir/KUL_main_functions.sh
cwd=$(pwd)
# FUNCTIONS --------------
# f... |
9d5d8e939688bf39b086e923989181420bef4515146d5139766d6a1176fb5c22 | Shell | 5,226 | 151 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
cd3f5b60d69d803f62c22b0798d9ff8889f2314e558dcf26bed69a3798118d67 | Shell | 5,438 | 191 | #!/bin/bash
# @ AR 04/02/2021
# this script will apply synb0disco without docker or singularity
# to do:
# inset exec_function
# insert loggin
# insert input arg parse
# insert function path, mrtrix, FS, ANTs finders
TOPUP=1
# This script needs to know
# where ANTs, FS, FSL and Synb0DISCO live
# define some vars
... |
2bae74dcc7331f8be283afb41e3b8028a28713b6f41cda74a5522393e7c4b27b | Shell | 5,496 | 66 | set -euo pipefail
: "${TCGA_DIR:=$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)}"
#数据预处理包括生成五折验证集和训练集
nohup python preprocessing_no_normalization.py > predata_no_nomalization_output 2>&1 &
nohup python preprocessing_cancer_single.py > predata_cancer_single_output 2>&1 &
#preprocess_1 五折数据
#preprocess_cancer_singl... |
47693919cff40782ae589a8ef46f179915f8c41b53a7b737afb60d44cd3907a4 | Shell | 5,589 | 238 | #!/bin/bash
# Bash shell script to process diffusion & structural 3D-T1w MRI data
#
# Requires Mrtrix3, FSL, ants
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
#
# v0.1 - dd 22/01/2019 - alpha version
v="v0.1 - dd 22/01/2019"
# Warps FA (and other) maps to MNI space
# - NNI warp is done by fmrirep on th... |
d12b903def7890ec881d07f4e6c242351332905e66c0d879c0819f876b5ee001 | Shell | 5,671 | 160 | #!/usr/bin/env bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
set -xv
# Given a name of a tool version variable, get the name of the tool version variable. The
# idea is that if the ... |
f4cc3ad55c036e9f55cae4afb262c1c61954341ca1ad761170c93825a132bfdd | Shell | 5,729 | 181 | #
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
source ${TOOL_WORKFLOW_LIB:?No TOOL_WORKFLOW_LIB}
testMarkWithPicard() {
assertFalse 1 markWithPicard
local markDuplicatesVariant=... |
a9946174fc520160810c8365c344d55f3d1a9a340b20f6d67ece8da7d095c9bd | Shell | 5,741 | 137 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
027fe66768444133d932b0e474bc41cf71be905a825e43bbe63e0e2d007da630 | Shell | 5,850 | 172 | #!/bin/bash
# This wrapper script is for running CUDA jobs (hint hint, OpenMM) on clusters.
# Command line switch indicates whether to do backups
do_bak=0
while [ $# -gt 0 ]
do
case $1 in
-b) do_bak=1 ;;
*) break ;;
esac
shift
done
# This is the command that we want to run.
COMMAND=$@
# ... |
49f7f1adc323e349a953971efee54fc8c67bd2dedfad5ac9f4ff29445d5891f9 | Shell | 6,069 | 164 | #!/bin/sh
# Wrapper script for docker.
#
# This is used primarily for wrapping the GNU Make workflow.
# Instead of typing "make TARGET", type "./run.sh make TARGET".
# This will run the make workflow within a docker container.
#
# The assumption is that you are working in the src/ontology folder;
# we therefore map the... |
feca46a1e07b85922b2e0ea73b154e775481e91875530cca82b77f758ee09bbd | Shell | 6,085 | 88 | #!/bin/env bash
s=$1
#Rapidtide is intended to be the FINAL step of a series.
#p40 of the users manual for rapidtide - we can regress with motfile or do oursleves beforehand. I am doing beforehand because rapidtide does not allow regression of powers - only 6 mot params and their derivs!
#Motion correction - Motion co... |
cf8d6006d308bca3992fd38de579b7bed83a8ba6d4bc21943ee55b310c9ed08d | Shell | 6,151 | 239 | #!/bin/bash
# Bash shell script wrapper for calling KUL_dcm2bids for multiple subjects
#
# Requires KUL_dcm2bids
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
#
# v0.1 - dd 26/10/2018 - alpha version
version="v0.1 - dd 26/10/2018"
# ----------------------------------- MAIN ----------------------------... |
bdc045f801e7352dae3cd443134492fd3a7d06399d2eaeece284f1d06024e7ca | Shell | 6,304 | 179 | #!/bin/bash
# changelog_generator.sh - Generate changelog with PR references and commit hashes
# Adapted for MosaiCatcher Pipeline with assembly-specific container tags
# Get range (can be tag, commit, or branch names)
PREVIOUS_TAG=${1:-""}
CURRENT_REF=${2:-HEAD}
# If no previous tag provided, find the last tag befor... |
608df5e8bdf2ec7ea8a273c81eb8f9131bc9549c54d4fa85067a0a38413efb25 | Shell | 6,323 | 38 | cmd_time=`TZ=UTC-8 date "+%Y%m%d-%H%M%S"`
# # NGNNDGCNN
# nohup python3 train.py --cmd_time ${cmd_time} --eval_hits_K 45 60 75 100 --device 0 --ngnn_code --ngnn_type input --num_ngnn_layers 1 --hidden_channels 96 --dataset ogbl-ppa --use_feature --epochs 4 --train_percent 60 --val_percent 40 --test_percent 1 --model ... |
f1586af28f0ea8720b222c634fa612b5b24dbb8535a6eff28345760f56da036b | Shell | 6,393 | 101 | #!/bin/env bash
#SBATCH --job-name=ME_Step2
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=15
#SBATCH --mem-per-cpu=14G
#SBATCH --time=30:30:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
fmriprep=/home/tconstab1/kg98_scratch/Toby/WHOL... |
92cd526b48e20e43a946c970b0afe74314e885ced886bd954824777b4b769aca | Shell | 6,414 | 243 | #!/bin/bash
# Bash shell script to create a lesion heat map after KUL_anat_segment_tumor
#
# Requires ants
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 01/05/2022
version="0.1"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir is made in m... |
3405452c50e383b344e77c6d9fe6b6b9106b8d8127e0739006557819c97c6dfc | Shell | 6,471 | 90 | #!/bin/env bash
s=$1
#p40 of the users manual for rapidtide - we can regress with motfile or do oursleves beforehand. I am doing beforehand because rapidtide does not allow regression of powers - only 6 mot params and their derivs!
#Motion correction - Motion correction is good since you want to actually be looking at... |
12c3acce8dc64851936636b96e44b13b5504b882e9d2654d7088b0b07b2f4358 | Shell | 6,581 | 198 | #!/bin/bash
################################################################################
# GenomeToWindows Installation Script
# Automatically sets up the required environment with all dependencies
################################################################################
set -e # Exit on error
# Colors f... |
7a123a5742f44d34e85814f7dbabfb70cfe3a2aceda4fc632939ee6a2684b75e | Shell | 6,753 | 283 | #!/bin/bash
#######################################
#
# Standard workflow for WoL + Woltka
#
#######################################
# Author: Qiyun Zhu
# License: BSD-3-Clause
# Version: 0.0.1-dev
# Email: qiyunzhu@gmail.com
# Last updated: 2021-04-22
# Usage: Customize the "Parameters" section, then run this scr... |
55bd7526994c383aa102e366d079eca69275475a25b87cbb2f1683a0c6110503 | Shell | 6,783 | 115 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
#PBS -l walltime=5:00:00
#PBS -l nodes=1:ppn=2
#PBS -m a
#PBS -l mem=8g
#PBS -j oe
# no BAM file is produced, everything is pip... |
1366fa8431c92adf5fb6df34a236d658e4e99a93cb57d94b6ad58ed560c8a43c | Shell | 6,811 | 210 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
09c5010bd0ce8dae0ce051c76d4a40f7055035a61bdb7ea0c30014bbceb2d687 | Shell | 7,322 | 243 | #!/bin/bash
set -e
########################################################################
# Package the binaries built on Travis CI as an AppImage
#
# For more information, see http://appimage.org/
########################################################################
# Output something before any command can fai... |
dd372182261e308fb2bc3dabcf7d153a09798e373e125d4c8a11e0c027debb9b | Shell | 7,435 | 169 | #!/bin/bash
#The default working directory should be "Glial_Chimera_scRNA_2020" folder if not otherwise mentioned
module load samtools/1.9
module load deeptools/3.5.1
module load bedtools/2.30.0
module load ucsc/b1
module load kentutils/302.1.0
#folder with gene and enhancer annotation files
inFolder="data_for_impo... |
57819954d70522e094e3b54e4cb7fbc419404e45e62a2d3d1fddb3984f85b695 | Shell | 7,507 | 227 | #!/bin/bash
# Copyright (C) 2025, 2026 Sotiris Lamprinidis
#
# This program is free software and all terms of the GNU General Public License
# version 3 as published by the Free Software Foundation apply. See the LICENSE
# file in the root directory of the project or <https://www.gnu.org/licenses/>
# for more details... |
0f852b208f7a54899b8ab2fa9c80d6a34dc01db684a2ac12cc713c45082305aa | Shell | 7,524 | 268 | #!/bin/bash
# Bash shell script to process diffusion & structural 3D-T1w MRI data
#
# Requires FSL, ants
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# @ Ahmed Radwan - UZ/KUL - ahmed.radwan@uzleuven.be
#
# v0.1 - dd 19/01/2019 - jurassic version
version="v0.2 - dd 22/12/2021"
kul_main_dir=$(dirname "$0"... |
cd3cb618571ff5b5cee9f241f9153434ed6850e34a7b323a360709d443a8c345 | Shell | 7,529 | 136 | #!/bin/env bash
SubjectList=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/410_clean_subjects_list.txt
PipelineLocs=(
'/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/NO_ME-ICA/NO_AROMA_or_FIX/Frist24'
'/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace... |
000cff837da1ee3f5f93f0cbce53657f31d71a4a6262a5541824d96daa423844 | Shell | 7,560 | 213 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
af7d767a5b30fd7b344ad630d6df263e8da0f7281bbf715ae5fcdbce013b872c | Shell | 7,727 | 335 | #!/bin/bash
# Bash shell script to visualise (f)MRI/dMRI results
#
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 11/10/2022
version="0.1"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir is made in main_functions
# FUNCTIONS -------------... |
64e4030555833fadea8f8dc9f2b613f061df2ddd5df59fb5f40153666101fa54 | Shell | 7,882 | 141 | #!/bin/env bash
s=$1
module load fsl
module load freesurfer
module load ants
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
wholebrain_mask_loc=${fmriprepDir}/sub-${s}/func/sub-${s}_task-rest_dir-RL_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
wm_probseg_loc=$... |
6738a184b8a3ff692f79d85ee7c8c2d61aa65d161c602c429a626db16008d3e0 | Shell | 7,919 | 174 | #!/usr/bin/env bash
# Build a portable Linux AppImage of the Miniscope DAQ.
#
# Mirrors the Windows release recipe (conda env from environment.yml), but builds
# USE_PYTHON=OFF (no embedded Python / DeepLabCut tracker — see BUILD_LINUX.md) so
# the bundle stays lean, then packages it with linuxdeploy + its Qt plugin.
#... |
f1f3897732d8664904017615d145a6605ac6a89ac6ea872a0f83038c4e517ad8 | Shell | 8,207 | 199 | #!/usr/bin/env bash
set -ue
if [ $# -lt 5 ]
then
echo "
SEACR: Sparse Enrichment Analysis for CUT&RUN
Usage: bash SEACR_1.3.sh <experimental bedgraph>.bg [<control bedgraph>.bg | <FDR threshold>] ["norm" | "non"] ["relaxed" | "stringent"] output prefix
Description of input fields:
Field 1: Target data bedg... |
a4e2cd6c86eca5397db6f66e1357469229a12458b2a474640162985ffe3fc7ae | Shell | 8,287 | 313 | #!/bin/bash
# Bash shell script to run synb0 from BIDS and store the output of topup in the BIDS derivatives
#
# Requires docker
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 06/09/2021
version="0.1"
kul_main_dir=`dirname "$0"`
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & ... |
97d031a5add947c8efefe447081a44685c6e9efc7bcb887f1a12c8d76ad3f844 | Shell | 8,296 | 258 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
b012624ca443c7ee272348c54a9989839b3e47c03bc444f113310deb1033433b | Shell | 8,424 | 132 | #!/bin/env bash
#SBATCH --job-name=fmri_prep
#SBATCH --account=kg98
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=16G
#SBATCH --time=24:00:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
#SBATCH --array=1-X
#Scr... |
51ccf34157684f69e998692148f7fe53e743a7c5438970e66ca585727b0673ca | Shell | 8,479 | 229 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
199bad03f271a26e83371c03944d5dc7463d1246f2fe81d726398fc5a4c6b26a | Shell | 8,938 | 281 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
dfab3d1545c2db33c46554c92d8824d4ee5cf738bd83561c27b70d26e5059aa4 | Shell | 9,024 | 282 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
d173ec927f3c14553c0ac0914d31feb0bce2c77298407ab9f45cbe91d6799569 | Shell | 9,289 | 293 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
1e193e5df4d808dabd272bd597f6d5ebca402ba5c69483d80cb2ecc6f716cb10 | Shell | 9,358 | 260 | #!/usr/bin/env bash
#
# This script updates ontology schema with ngram based new search fields. These new text fields has naming: *_autosuggest_e
# and *_autosuggest_wse, and enable partial matching capability. To run this script, your solr should be up and running
# and the latest dump file, solr.json, is uploaded.
#
... |
d3e3e6427b169d0ec9a5189106b663dad8cde31be4d041da52c508912b4d680f | Shell | 9,373 | 275 | #!/bin/bash
#SBATCH --job-name=process_samples
#SBATCH --output=logs/process_samples_%a.out
#SBATCH --error=logs/process_samples_%a.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=24:00:00
#SBATCH --partition=workq
#SBATCH --array=1-34%10 # Update based on the numbe... |
6516edda6f803e0be25449e977649400621b178ca5014c3461cc8075d655c776 | Shell | 9,791 | 326 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
930414a0b0971e27be09e7fa1f8cab5239f54018e5fda3dbaed8d1247986b16d | Shell | 9,873 | 328 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
55be0d3512d7a63ccdd38d8820a9571d1cf604a3e939904ef4c746421a5062d7 | Shell | 9,966 | 416 | #!/bin/bash
# Bash shell script to prepare fMRI/DTI results for Brainlab Elements Server
#
# Requires Mrtrix3, Karawun
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 12/11/2021
version="0.3"
kul_main_dir=`dirname "$0"`
source $kul_main_dir/KUL_main_functions.sh
cwd=$(pwd)
# FUNCTIONS --------------
# f... |
dde8be9139ec72c5907fc9373a5d41f109d7e7a3635a46a885f317fa658665cf | Shell | 10,127 | 322 | #!/bin/bash
# Bash shell script to analyse DTI
#
# Requires fmriprep
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 18/05/2022
version="0.1"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir is made in main_functions
# FUNCTIONS -----------... |
b1a195c42cb72205ab93780dd0aeb8b0911150b7b968ed4bd22667fc0ef39e2e | Shell | 10,157 | 277 | #!/usr/bin/env bash
# pull_containers.sh
#
# For a given MosaiCatcher release:
# 1. Clone the git tag into STABLE_BASE (default: /g/korbel2/$USER/workspace/StrandSeq_workspace/STABLE)
# including all submodules (.tests, workflow/data)
# 2. Pull the matching Apptainer/Singularity containers from GHCR
#
# Design... |
13a4eadb6a6a225b4437bfef92a2884d26193af7da6298ebf2d9371f9b539df0 | Shell | 10,217 | 336 | #!/usr/bin/env bash -l
#
# AI tools for perinatal brain MRI analysis
#
# Copyright 2026 - King's College London
#
# The auto SVRTK code and all scripts are distributed under the terms of the
# [GNU General Public License v3.0:
# https://www.gnu.org/licenses/gpl-3.0.en.html.
#
# This program is free software: you c... |
0e0447106131c23e7e6a3b33a57c4982c1089b20479f845c9c3adf728676c67c | Shell | 10,518 | 344 | #!/usr/bin/env bash
#
# run_intergenic_distance_pipeline.sh
#
# Compute intergenic read distance histograms stratified by gene class.
#
# Pipeline Overview:
# 1. Parse GTF to extract gene coordinates with biotype and 3'UTR annotations
# 2. Filter BAM files (remove unmapped, secondary, duplicates; MAPQ >= 30)
# 3.... |
987651a97d1ae97cca5baf852c77b42f282b3fe27481fb16b62611a8e170616f | Shell | 11,456 | 484 | #!/bin/bash -e
# Bash shell script to run qsiprep or mrtrix_connectome
#
# Requires docker
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 19/03/2021
version="0.1"
kul_main_dir=`dirname "$0"`
source $kul_main_dir/KUL_main_functions.sh
cwd=$(pwd)
# FUNCTIONS --------------
# function Usage
function Usage... |
733832213527a99484c585bf66158cb09f4f9214873958f6b71ab1410b950754 | Shell | 11,624 | 339 | #
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
##############################################################################
## Domain-specific code
#######################################... |
7f990d194b2319e76d4d2434087a593e550f155a7534acaf70d9f72e98e26ce3 | Shell | 11,630 | 375 | #!/bin/bash
# Bash shell script to process diffusion & structural 3D-T1w MRI data
#
# Requires Mrtrix3, FSL, ants
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# @ Ahmed Radwan - UZ/KUL - ahmed.radwan@uzleuven.be
#
# v0.1 - dd 19/01/2019 - jurassic version
version="v0.2 - dd 05/12/2021"
kul_main_dir=$(dir... |
6a748e6945304a48aa1c746e73862e2292c8c323317ca4364f5045f55d48005f | Shell | 11,825 | 349 | ## Install dependencies on Ubuntu or OS X (using Homebrew)
norm_option_value()
{
if [ "$1" = on ] || [ "$1" = ON ] || [ "$1" = yes ] || [ "$1" = YES ] || [ "$1" = y ] || [ "$1" = Y ] || [ "$1" = 1 ] || [ "$1" = true ] || [ "$1" = TRUE ]; then
echo ON
elif [ "$1" = off ] || [ "$1" = OFF ] || [ "$1" = no ] || [ ... |
89d3ecd26b309cb56749a528ece5116d57f28583c2a821f59c6db7003fb8e48d | Shell | 11,902 | 333 | #!/bin/sh
# Convert ANSI (terminal) colours and attributes to HTML
# Licence: LGPLv2
# Author:
# http://www.pixelbeat.org/docs/terminal_colours/
# Examples:
# ls -l --color=always | ansi2html.sh > ls.html
# git show --color | ansi2html.sh > last_change.html
# Generally one can use the `script` util to cap... |
c28a68a77df4c665a5c92352f8d68a9efdb7515126821a0872ec85291136cb0d | Shell | 12,497 | 181 | #!/bin/env bash
#SBATCH --job-name=tedana
#SBATCH --account=kg98
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=12G
#SBATCH --time=03:30:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
#SBATCH --array=1-X
#Scri... |
e1a6a9a6523bb6fcd8c4ab4096d4258107c27015f9bc38da3febe1b70cca3748 | Shell | 12,659 | 323 | echo "Begin"
date
RootPath="/public/home/lishr2022/Project/Cross-modal/Preprocess"
# ÐÞ¸Ä
echo "¹¤×÷Ŀ¼: $1"
# ÐÞ¸Ä
ResultsPath=$1 #ResultsPathÊÇÊý¾Ý´¦Àíºó×îÖÕ±£´æµÄλÖÃ
T1=$2
PhaseAP=$3
PhasePA=$4
starttime=$5
num_volumes=$6
subject=$7
subject_name=${subject:3}
cutAP=${ResultsPath}/cutAP.nii.gz
cutPA=${Result... |
dea7bd1ea1a1f8ee9c8d7eb438e696a67ab8640fa36dd9b908509db8a83b185e | Shell | 13,079 | 343 | #!/bin/bash
set -e
if [[ $# -lt 12 ]];then
echo "usage: sh $0 -genomeSize -splitCount -maskFile -fq1 -fq2 -speciesName -tissueType -refIndex -annotationFile -imageRecordFile -imageCompressedFile -sif -threads -outDir
-genomeSize : genome size
-splitCount : count of splited stereochip mask file, usually 16 ... |
c01915d3ca68c4873f5f4e2eeab80c32e79ece5a0cbcaec41e281e50d90070ca | Shell | 13,090 | 274 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
source "$TOOL_WORKFLOW_LIB"
printInfo
set -o pipefail
ID=${RUN}_${LANE}
SM=sample_${SAMPLE}_${PID}
# RODDY_SCRATCH is used ... |
5c9d186578f7ba7dd06f391960b4f359e9e1582a445cc897f7a340309316f4d9 | Shell | 14,250 | 276 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
source "$TOOL_WORKFLOW_LIB"
printInfo
set -o pipefail
ON_CONVEY=${useAcceleratedHardware:-false}
ID=${RUN}_${LANE}
SM=sample_$... |
11f142f80230abd07948af862eeeb7dce01a87afe18f1c5dc2f58f6cd1c329c1 | Shell | 14,325 | 514 | #!/bin/bash -e
# Bash shell script to process diffusion & structural 3D-T1w MRI data
#
# Project PI's: Stefan Sunaert & Bart Nuttin
#
# Requires Mrtrix3, FSL, ants, freesurfer
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
#
# v0.1 - dd 14/02/2019 - alpha version
v="v0.1 - dd 14/02/2019"
# A few fixed (f... |
9ef09bb35eef418a7477b8c04723daf9ae0a16b7e938b8eb1687f13f9d67dc49 | Shell | 14,863 | 417 | #!/bin/bash
# Bash shell script to:
# - define global functions used by all /DATA/fmri_pats/BIDS/derivatives/KUL_compute/sub-Casier/FastSurfer/sub-Casier/scripts/lh.processing.cmdfsub-scripts
# - define defaults
# - execute startup
#
# @ prof.sunaert@gmail.com - v0.2 - 18/11/2021
# MAIN FUNCTION - Function task_ex... |
120a509246a3648173b70fd16d6b9240ab7d544bf89c43b54a5f72b8f04f05a1 | Shell | 15,486 | 483 | #!/bin/bash
################################################################################
# Genome Window Generator v1.1
# Part of the MethylSense package
#
# This script downloads genomes from Ensembl or UCSC and generates genomic
# windows of specified sizes using bedtools.
#
# v1.1 - Added --genome flag for dire... |
d1ce83550531af24f0857ac0c21313894c1046cfe89884c4695dba95d4bd6fa0 | Shell | 15,500 | 533 | #!/bin/bash
# Bash shell script to register BIDS data to the T1w
#
# Requires ants
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 18/02/2022
version="0.1"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir is made in main_functions
# FUNCTIO... |
0c291be8179034e1e010c13c515f57b6305b61dd45b4d97bdffa1137cc79a62e | Shell | 15,614 | 223 | #!/bin/env bash
s=$1
module load fsl
module load freesurfer
module load ants
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
wholebrain_mask_loc=${fmriprepDir}/sub-${s}/func/sub-${s}_task-rest_dir-RL_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
wm_probseg_loc=... |
c8438187d07887195a20b6fc8f1d2fbeea6478d39676a82c34f50197da29dd85 | Shell | 17,239 | 422 | #!/bin/bash
set -e
if [[ $# -lt 12 ]];then
echo "usage: sh $0 -genomeSize -splitCount -maskFile -rnafq1 -rnafq2 -adtfq1 -adtfq2 -proteinList -refIndex -annotationFile -speciesName -tissueType -rRNAremove -imageRecordFile -imageCompressedFile -sif -threads -outDir
-genomeSize : genome size
-splitCount : cou... |
db1af7babee4ed9796eeb92dcfccb12e3d7035ff0f359481920d762a46235700 | Shell | 18,186 | 403 | #!/bin/bash
# Auto-detect location of the toolbox bin directory
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
TOOLBOX_BIN="${SCRIPT_DIR}/functions"
export TOOLBOX_BIN
# -----------------------------
# Microstructure Profiling Toolbox Wrapper
# -----------------------------
show_help() {
echo "Usage: ... |
bfa85abf5243d387b857555f6c4704eed87f3fa7e9466a292f3e99becd13c6a3 | Shell | 18,396 | 577 | #!/bin/bash
# Bash shell script to segment a tumour and/or resection cavity
#
# Requires HD-GLIO-AUTO, HD-BET, resseg
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 14/02/2022
version="0.1"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir i... |
08d2364b4815bd8090139ac0f450a3144a48b63b51801bda546ba3512e98f97c | Shell | 19,721 | 496 | #!/bin/bash -e
# Sarah Cappelle & Stefan Sunaert
# 19/01/2021
# This script is the first part of Sarah's Study1
# This script computes a MS lesion map using freesurfer samseg
#
version="0.9"
kul_main_dir=$(dirname "$0")
script=$(basename "$0")
source $kul_main_dir/KUL_main_functions.sh
# $cwd & $log_dir is made in ma... |
d2c44445fe6373dd6a965f0bb7f6022e9002b6d826886c1fbfcfa12df20d09a6 | Shell | 19,795 | 397 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
source "$TOOL_WORKFLOW_LIB"
printInfo
set -o pipefail
today=`date +'%Y-%m-%d_%Hh%M'`
# RODDY_SCRATCH is used here. Is for PBS ... |
0445c45ee92bd197dd37f15fcc78d166f10e863e7238a9e4fb8882ed93aa6874 | Shell | 23,489 | 801 | #!/bin/bash -e
# Bash shell script to process diffusion & structural 3D-T1w MRI data
#
# Requires Mrtrix3
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
#
# v0.1 - dd 16/04/2019 - alpha version
v="v0.1 - dd 16/04/2019"
# ----------------------------------- MAIN -----------------------------------------... |
b513032be688687c1767d14a93539e04d2256eb956f1063c77e7cf07aac63c80 | Shell | 23,958 | 609 | #!/bin/bash
# Bash shell script to process diffusion & structural 3D-T1w MRI data
#
# Requires Mrtrix3, FSL, ants
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
#
# v0.1 - dd 09/11/2018 - alpha version
version="v0.4 - dd 04/12/2021"
# To Do
# - register dwi to T1 with ants-syn
# - fod calc msmt-5tt in s... |
ecfa8922165cf48b713e69c4b632c42df535e22ac969c79b6f8d1fa78481ca0f | Shell | 24,662 | 557 | #!/bin/bash
set -e
if [[ $# -lt 12 ]];then
echo "usage: sh $0 -SN -dataDir -registJson -speciesName -tissueType -outDir -imageRecordFile -imageCompressedFile -doCellBin -threads -sif
-SN : sample id
-dataDir : output directory of gene expression matrix result
-registJson : manual registration json fil... |
cd5590f369fd2f4a4ee6731716c1c0ecde14830317a9acee13f7a78a86bd8e4d | Shell | 24,761 | 793 | #!/bin/bash
# NanoporeToBED Pipeline - Unified Intelligent Setup
# Automatically detects platform and chooses optimal installation strategy
# Supports: Linux x86_64, macOS Intel (x86_64), macOS ARM64 (Apple Silicon)
set -e
echo "=========================================="
echo "NanoporeToBED - Intelligent Setup"
ech... |
0cdfc4c3522fa4356e2e0870cf8e14742d6d7892d8fb45f286e5a8a126ac2f2c | Shell | 26,192 | 819 | #!/bin/bash
# NanoporeToBED Pipeline
# Version: 1.5.0
#SBATCH --job-name=NanoporeToBED
#SBATCH --output=NanoporeToBED.out
#SBATCH --error=NanoporeToBED.err
#SBATCH -c 40
#SBATCH --mem 192g
#SBATCH --time=72:00:00
#SBATCH --account YourAccount
VERSION="1.5.0"
# Environment
cd $HOME
source ~/.bashrc
micromamba activa... |
054d767be208940502ea5db1935c2618e87637ce15bc6ca7b0b8b0c4d997758b | Shell | 27,411 | 856 | #!/bin/bash -e
#set -x
# Bash shell script to process diffusion & structural 3D-T1w MRI data
#
# Requires Mrtrix3
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# @ Ahmed Radwan - KUL - ahmed.radwan@kuleuven.be
#
# v1.0 - dd 19/11/2021 - beta version
v="v1.0 - dd 19/11/2021"
# Changes made by AR:
# 1- Upd... |
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