sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
d2a98e057a7068dbb7f488d9248b9df867ab1754ddfd6048eef90870fe0d771a | Shell | 2,632 | 30 | #!/bin/bash
#SBATCH -p gpupar
#SBATCH --cpus-per-task 4
#SBATCH --gres=gpu:1
#SBATCH --nodelist gpu02
#SBATCH --mem=64G
#SBATCH -o ./slurm/slurm%A_%a.out
#SBATCH -e ./slurm/slurm%A_%a.err
#SBATCH --array=0%1
cmdlines=(
"python -m A01_ImageNet.main -ne 5 -bs 512 -lr 0.001 -nc 1000 -ss 20 --dataset imagenet1k --mode... |
30549fd0f1909bfab9541814ed3989bd03283218708db9f8bd607c1300c1fbb9 | Shell | 2,633 | 130 | # set variables for alignsurface.sh script
subjnum=$1
subjprefix=s
if [ "$subjnum" = "" ]; then
echo "ERROR: No subject id given"
exit 1
fi
#subjnums="05 03 04 02 06 07 08" # now set in the script itself
subjid=${subjprefix}${subjnum}
cd ..
rootdir=`pwd`"/"
if [ `echo $rootdir | wc -w ` -ne 1 ]; then
echo "r... |
7ad4badd210b5e61f3f69956eb2666a1bb456f1bdf89255235560cebabb65c61 | Shell | 2,638 | 72 | #!/bin/bash -e
# DIAMOND protein sequence aligner
# Copyright (C) 2012-2026 Benjamin J. Buchfink
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your... |
ea82dd205231e5685fc8630e74c238f0ff143a28434c0f17c93810360262eeb1 | Shell | 2,651 | 85 | #!/bin/bash
set -e
set -o pipefail
# Use the OpenPedCan bucket as the default.
URL=${OPENPEDCAN_URL:-https://s3.amazonaws.com/d3b-openaccess-us-east-1-prd-pbta/open-targets}
RELEASE=${OPENPEDCAN_RELEASE:-v15}
PREVIOUS=${OPENPEDCAN_RELEASE:-v14}
# Remove old symlinks in data
find data -type l -delete
# The md5sum fi... |
17224473c699f3af7229facae22d5e3e0686fca12cc2cd6af1d0a973d953ab1a | Shell | 2,656 | 56 | #!/bin/bash
# Define paths
ROOT=/home/user/Documents/fMRI_Exp
SUBJECT=19
if [ "$SUBJECT" -lt 10 ]; then
SUBJECT="0${SUBJECT}"
echo "add zero"
fi
echo "cur_subject is ${cur_subject}"
FUNC_IMAGE=/home/user/Documents/fMRI_Exp/example_func_all_old/sub-$SUBJECT/example_func.nii
OUTPUT_DIR=$ROOT/MPRAGE_struct_s_only/sub$... |
6848865ba43a2c95e1dd93b016fde0505aa27dafb161865ad2a6127a258abced | Shell | 2,659 | 76 | #!/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
######################
# setup f... |
07df2816be50e5cf13608fe228a8ac5dca74b46fcff78801cb953b52e545c8da | Shell | 2,662 | 128 | #! /bin/bash
set -e
visual_agg() {
local m=$1
shift 1
sleep 10
python -m rscvp.statistic.$m \
-D 210315,210401,210402,210409,210402,210407,210409,210416,210604,210610,210514,210519,211202,211209,211203,211208,211202,211208,221018,221019 \
-A YW006,YW006,YW006,YW006,YW008,YW008,YW008,YW008,YW010,YW010,YW... |
bbce85d33cf68be3f97bcc608454918a58d7785c0cf426dc666c597637d4a432 | Shell | 2,667 | 69 | #!/bin/bash
# PediatricOpenTargets 2021, 2022
# Yuanchao Zhang, Jo Lynne Rokita
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/run_in_ci.sh
script_directory="$(perl ... |
a8fb7634a0c54913f9773451828d9b91a26362c9f55cffc8db7a3f96dfb4f4da | Shell | 2,697 | 76 | #!/bin/bash
# K S Gaonkar
# Run fusion_filtering
# Takes one environment variable, `OPENPBTA_BASE_SUBTYPING`, if value is 1 then
# uses pbta-histologies-base.tsv for subtyping if value is 0 runs all modules (Default)
# with pbta-histologies.tsv
set -e
set -o pipefail
RUN_FOR_SUBTYPING=${OPENPBTA_BASE_SUBTYPING:-0}
... |
3e37031f640ae95ae60d6245d79f054e499aac5aae790734c03f7d934f4123a4 | Shell | 2,698 | 69 | #!/bin/sh
# warp fresults from subject funtional space into standrad space
output_dir=$1
inital_ana_name=$2
vnapr=(18 19 20 21 22 24 25 26 28 29 30 31 32 34 35 36 37 38 40 42 43 44 45 46 48 49 50 51)
# Define paths
root=/data/holly-host/smark/fmri_sub_preproc_dir
#analysis_dir=$root/PileNregNativecleaned_MotionCSFonly... |
8cfc10f49841de116dd9c48e951449b1aedd9c69ac6c9d7792bf52782abeedd3 | Shell | 2,709 | 67 | ###############################################
# Shell script for EAT RNA-Seq data analysis
###############################################
## Prerequisite
## The folloing software should be available in the current environment
## fastqc, multiqc, samtools, hisat2, trimmomatic
## Create subdirectories
fastq_dir="fa... |
3e3f547eea8227e7c5a40b5b55573e2c7ab17340be8a216659d3c44d26e04211 | Shell | 2,720 | 86 | #!/bin/sh
set -e
# Defaults (mirror finetune_unfreeze_backbone_multitarget.sh)
MASTER_PORT=10021
MASTER_IP=127.0.0.1
n_gpu=$(nvidia-smi -L | wc -l)
nnodes=1
node_rank=0
exp_name=multitarget
run_name=bs_2_unfreeze_backbone
data_path="../xtb_to_dft_implicit/split_1"
user_dir="./unimol_plus"
arch="uniprop_small"
subse... |
5fa31b1444b4f9b4642edf4aedcf4ce7ecfd8c70cd54fe9507499d23d1196a2b | Shell | 2,725 | 79 | #!/bin/bash
# preprocess for probtrackX
process_subject() {
FS_OUTPUT=$1
T1w_PATH=$2
FA_PATH=$3
SEED_PATH=$4 # in FA/DTI space
OUTPUT_DIR=$5
# Get the transformation matrix between T1w, freesurfer and diffusion
tkregister2 --mov "${FS_OUTPUT}/mri/orig.mgz" \
--targ "${FS_OUTPU... |
39cb6bcbc37fe707b1e75173b81e4c884c4a07de9e7340c7b31ae9e5013b1834 | Shell | 2,749 | 71 | #!/bin/bash
set -e
set -o pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# This option controls whether on not the step that generates the EPN only
# files gets run -- it will be turned off in CI
SUBSET=${OPENPBTA_SUBSET:-1}
# Define needed files
HISTOLOGIES=.... |
add5a0a98a844aa23144b224bf4cde7136395f50b619fe37b07d3a4c40055de7 | Shell | 2,749 | 71 | #!/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... |
31543cd22a07d111d38fd2292520ee4a096a3f35b31da54d97da832947e896fa | Shell | 2,752 | 19 | module purge
module load Python/3.9.6-GCCcore-11.2.0
time srun -A ec12 --time=0-10:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-node=1 ~/.local/bin/nrniv FFI_BS_single_stimulation_IClamp_500axon_240610h.hoc &
time srun -A ec12 --time=0-10:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-node=1 ~/.l... |
b58c6af478c0531ace8e4703b3d3833e16111b78006dff5f2ed7395b6ab21e1f | Shell | 2,755 | 69 | # run ensemble_predict_heteroscedastic_ResidualBind.py with both --distill and --eval flags set
# runs ensemble_predict_heteroscedastic_ResidualBind.py in distill mode
# for ensemble of ResidualBind models trained with heteroscedastic regression
# toggle DOWNSAMPLED to control whether distilled training data is obtain... |
6e962551d410313ae00fba1034f74a8e5e6f91ec5843de58699f49ab98d273f3 | Shell | 2,760 | 133 | #!/bin/bash
#
# Author(s): Timothy B. Brown (tbbrown at wustl dot edu)
#
#
# Function description
# Show usage information for this script
#
usage() {
local scriptName=$(basename ${0})
echo ""
echo " Usage ${scriptName} --studyfolder=<study-folder> --subject=<subject-id> --taskname=<task-name>"
echo ... |
1ecd3b2c5df47e3ecd8c45606a7551957322e8e836e5a183b260c0755fa3f6ec | Shell | 2,763 | 87 | #!/bin/bash
# outdir="${3:-.}"
# mkdir -p "$outdir"
# fNameBase=$(remove_ext $1)
# nVols=$(fslinfo ${fNameBase} | grep ^dim4 | awk '{print $2}')
# if [ -z "$2" ]
# then
# base=$(expr ${nVols} / 2)
# else
# base=$2
# fi
# 3dvolreg -prefix "$outdir/${fNameBase}_mc.nii" \
# -Fourier \
# -flo... |
209f4e7a0a390a7fd50b6c74fcca16e3f350ca272313285b832f7f2818b7bdbb | Shell | 2,785 | 40 | #enviroment settings
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(abs_path(@ARGV[0]));' -- "$0")"
cd "$script_directory" || exit
#generate collapsed data for co... |
0db4a9f8d0b4f68331b7f3992be7785ac103f8e9883a8be6b77bf1c9580d21b0 | Shell | 2,795 | 20 | module purge
module load Python/3.9.6-GCCcore-11.2.0
time srun -A ec12 --time=0-10:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-node=1 ~/.local/bin/nrniv FFI_BS_single_stimulation_IClamp_10axon_NA_240610e.hoc &
time srun -A ec12 --time=0-10:0:0 --mem=64G --ntasks=1 --cpus-per-task=32 --ntasks-per-node=1 ~/... |
748d368503b5efed65eabb7f3c59c9502b8f4eedd07bec3d6201dce5683a50b3 | Shell | 2,805 | 112 | #!/bin/bash
# base name of the bench
# it reads $1.out
# and generates $1.pdf
WHAT=$1
bench=$2
settings_file=$3
header="rev "
while read line
do
if [ ! -z '$line' ]; then
header="$header \"$line\""
fi
done < $settings_file
echo $header > $WHAT.out.header
cat $WHAT.out >> $WHAT.out.header
... |
9bed0b157dafc27bdfaf49b1aea9b2a1a7daf65a5f616c338782e4422a6c670b | Shell | 2,810 | 93 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
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 ${numArgs} ]; do
argument=$... |
f5b854341712623ba324bfec994204a5df43ac14cd657b4f8069950c9b985052 | Shell | 2,814 | 94 | #!/bin/bash -l
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-gpu=40gb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --partition=gpuq
#SBATCH --time=00-23:59:59
#SBATCH --output=job_default.out
# Function to parse named arguments
parse_args() {
while [[ "$#" -gt 0 ]]; do
case $1 i... |
69e5fa642eabd3b51e703446a92f40b02594d6952b715b5475fda0e35146f4c4 | Shell | 2,815 | 83 | #!/bin/bash
# PediatricOpenTargets 2021
# Yuanchao Zhang
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from the run_in_ci.sh file at
# <https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/>
script_directory="$(perl -e 'us... |
12b4906bd99b2139f4a499a2fb955ef93195e27f90d5b7884d8a272713e5aa3f | Shell | 2,835 | 56 |
#!/bin/bash
source /cbica/projects/luo_wm_dev/miniconda3/etc/profile.d/conda.sh
conda activate babs
# ---------
# HCPD - noddi
# ---------
cd /cbica/projects/luo_wm_dev/input/HCPD/derivatives/
babs-init --where_project /cbica/projects/luo_wm_dev/input/HCPD/derivatives/ \
--project_name babs_noddi \
--input... |
115ae353444ff1c011f402c4cc212ba060aa6328100eeb18324b4996bfa54955 | Shell | 2,838 | 185 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
# which machine
if [[ $(hostname) == "bkrunch-linux" ]]; then
OUTPUT="/scratch/data/user/yuting/analysis/phys"
elif [[ $(hostname) == "bkrunch2" ]]; t... |
463afe8dde5083f6bb3f261fa88be0b5775241627ef11fd512a15968f52e505e | Shell | 2,838 | 66 | #!/bin/bash
# script to estimate rotations between MNI and FS_LR space
# output: affine transforms that will be used to pre-initialise alignment to template for all native surfaces
# example call:
Usage() {
echo "estimate_pre_rotations.sh <MSM bin> <MNI surf> < MNI data> <target surf> <target data> <outdir> <... |
d924ca605a7468af056e8ba36117c1393a2b6b678c41075edb174880ad7dbe4d | Shell | 2,839 | 89 | # ===== SET UP =====
#set -ueo pipefail
if [ $# -ne 1 ]; then
echo -e "Usage: $0 <input_data_and_params>"
exit 1
fi
echo -e "#=====================\n#"
echo -e "# $(basename "$0") \n#"
echo -e "#=====================\n#"
# Read input config
neda=$(dirname $(dirname "$0"))
source $neda/scripts/process_input.s... |
fa6deca276eb478572444aa1aaeefcc73316719f58ee60e58a4514733b68b025 | Shell | 2,858 | 100 | #!/bin/bash
set -euo pipefail
bids_dir="$1" # BIDS root directory, e.g. /mnt/f/BIDS/WCH_SVD_3T_BIDS
subject_id="$2" # Subject ID without "sub-", e.g. SSI0188
#######################
# Prepare directories #
#######################
subject="sub-${subject_id}"
fs_root="${bids_dir}/derivatives/freesurfer"
subje... |
594847dbe04c615bf924077e7ca4ee44ffac06efa39400a1304a10ee9f237dc4 | Shell | 2,865 | 73 | #!/bin/bash
# The input data should have been filtered against blacklisted regions
usage()
{
echo "$(basename "$0") [-h] INTERS DNASE TFPEAKS NAME DATADIR"
echo "-- Progam to preprocess the interactions and generate negative samples."
echo "where:"
echo "-h show this help text"
echo "INTERS ... |
c9fd39da25a49490e648d8da0277afb6642d5588610dbfc9b587b1287e7e8b32 | Shell | 2,866 | 87 | #!/bin/sh
set -e
# Defaults (mirrors validate_multitarget.sh but for single-target absorption)
MASTER_PORT=10022
MASTER_IP=127.0.0.1
n_gpu=$(nvidia-smi -L | wc -l)
nnodes=1
node_rank=0
exp_name=singletarget
run_name=final_xtb_to_dft_implicit
data_path="/home/potapov/nablaColors/unimol_plus/absorption/xtb_to_dft_imp... |
6738197f0141c2a6b60acbf6d49852bb49ede55874f0d18b8e91e7aa8bf6e255 | Shell | 2,876 | 78 | #!/bin/bash
# CCDL for ALSF 2020
# Candace L Savonen
#
# Set this so the whole loop stops if there is an error
set -e
set -o pipefail
# Need to adjust minimum samples to plot if in CI:
IS_CI=${OPENPBTA_TESTING:-0}
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# Data an... |
4b502b543b763f7dedaf7ec5dc0e1e158ab2693ff4add6356e35a9ac2435e20d | Shell | 2,882 | 90 | #! /bin/bash
#
# This is a shell script to register T1w image to MNI 2009c
#
# Dependencies: (1)ANTs
#
# Creator: Kwok-shing Chan @DCCN
# kwokshing.chan@donders.ru.nl
# Date created: 6 October 2022
# Date edit: 15 June 2025
############################################################
# export ITK_GLOBAL_DEFAULT_NUMBER... |
d6779b5bbb8823b6fa880b3b6b6cfb01ea9664967c32d053b457079db2ca48e2 | Shell | 2,884 | 80 | #!/usr/bin/env bash
# Checks for the multi-sample run (four samples, per-sample references).
# Run with the working directory set to fire-test-data after `pixi run test-multi`.
set -euo pipefail
V="v$(echo "$PIXI_PROJECT_VERSION" | cut -d. -f1-2)"
FAILURES=0
assert_genome() {
local sm=$1 name=$2
local genomes... |
5a05fc370ec5e3eeabb3a10f9f72b43f8d5ea28145902d7e41af96a1313df3e2 | Shell | 2,886 | 72 | #!/bin/bash
# ScaleVolumeNHP.sh
# Scale volume for NHP FreeSurfer
# The script calculates a scaled volume to be used for FreeSurfer. Scaling factor is usually set by the number larger
# than 1 for small brain, and useful for NHP brain. The brain of the output volume is enlarged by the scaling factor
# with the same loc... |
9bf8c16ad20a4dd05fc4e6579a71d10e7783c9892a5e6820831e4caf51792863 | Shell | 2,893 | 91 | #!/bin/bash
# Requirements for this script
# installed versions of: FSL
# environment: HCPPIPEDIR, FSLDIR
# ------------------------------------------------------------------------------
# Usage Description Function
# ------------------------------------------------------------------------------
script_name=$(ba... |
f1896f9ca6b431710f76e20caed2e9af73cc139cb631fa4d840dffb611252cdf | Shell | 2,909 | 107 | #!/usr/bin/env bash
'''
./run_mrtrix_tractography.sh \
/Volumes/Flashy/HIE_FBI_003/FBWM_b4000/metrics \
/Volumes/Flashy/HIE_FBI_003/FBWM_b4000/wm.nii \
/Volumes/Flashy/HIE_FBI_003/FBWM_b4000/wm.nii \
/Volumes/Flashy/HIE_FBI_003/FBWM_b4000/metrics \
SD_STREAM
'''
set -euo pipefail
METRICS_DIR="${1:?Usage: run_mrtrix_t... |
4964bf59586f6d92b52c5f2adb955850b9e18a636e50eda619e12e6ffac1d9a8 | Shell | 2,916 | 77 | #!/bin/bash
# Register one modality to another with optional skull stripping
process_subject() {
IMAGE_TARGET=$1
IMAGE_TARGET_STRIP=$2
IMAGE_SOURCE=$3
IMAGE_SOURCE_STRIP=$4
FLIRT_DIRECTION=$5
OUTPUT_DIR=$6
REGISTERED_IMAGE_NAME=$7
SOURCE_TO_TARGET_MAT=$8
TARGET_TO_SOURCE_MAT=$9
... |
9dbebe4056e6649c31225a288a37ea0eed9cf34894ea4b12ef4fe5ad73308cf7 | Shell | 2,941 | 59 | #python -u generate_dataset.py --num-train 5000 --seed 43 --n_isolated 5 --n_stick 0 --n_hinge 0 --n_workers 50
#
#python -u generate_dataset.py --num-train 5000 --seed 43 --n_isolated 1 --n_stick 2 --n_hinge 0 --n_workers 50
#
#python -u generate_dataset.py --num-train 5000 --seed 43 --n_isolated 2 --n_stick 0 --n_hin... |
5db3bfd7212e986e2b8b78d98a471e47991306ad4b764679a551ab81c331bb7c | Shell | 2,943 | 87 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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"... |
fa67caa55661791d1472cc955fe8feaf8148616cd67e81178ce1feba9665d260 | Shell | 2,962 | 87 | #!/usr/bin/env bash
# Run Parsl + EnsembleLauncher demo (5-molecule thermo screen, MACE on CPU)
# on a Crux compute node.
#
# Must be executed INSIDE an interactive PBS allocation on Crux:
# qsub -I -A <proj> -l select=1 -l walltime=01:00:00 -q debug
# cd /lus/eagle/projects/ChemGraph/thang/ChemGraph
# bash scrip... |
b16635b299c5cbf696f5b515fdf9c0843c44da31e8072d1c88aede17f414cbd8 | Shell | 2,965 | 82 | #!/bin/bash
# Evaluation script for mcmlnet gpumcml data generation
set -e # Exit on any *unexpected* error
set -o pipefail
# Colors
RED='\033[0;31m'; GREEN='\033[0;32m'; YELLOW='\033[1;33m'; BLUE='\033[0;34m'; NC='\033[0m'
print_status() { echo -e "${BLUE}[INFO]${NC} $1"; }
print_success() { echo -e "${GREEN}[SUC... |
13876ac6c83a531362d85f8988e5afa1d379df830affd200cf47d95545922195 | Shell | 2,983 | 129 | #!/usr/bin/env bash
set -e
# Default values
t1=""
mni_template=""
t1_mni_out=""
brain_mask_out=""
t1_2_mni_warp=""
mni_2_t1_warp=""
t1_stripped=""
t1_stripped_out=""
register_between_stripped=false
# Parse arguments
while [[ $# -gt 0 ]]; do
key="$1"
case $key in
-t1)
t1="$2"
shift; shift
;;
... |
c263e6ce384645b18e51548cce9a5ea4d0fe147a0122c7027b938e4f80043ebd | Shell | 3,000 | 99 | #!/bin/bash
# This is small script that copies all necessary input data of my ocular dominance
# columns project and stores it into a common output directory. Valid session names are
# GE_EPI<n>, SE_EPI<n> or VASO<n>. When notnulled is set to notnulled, the not-nulled
# time series from the VASO measurement is copied... |
8ec5ca98d0404485d43671e2abc4cfce66c30ca642e1cce96d3e6e6c60d73f53 | Shell | 3,002 | 89 | #!/bin/bash
#
# # Compile_MATLAB_code.sh
#
# Compile the MATLAB code necessary for running Resting State Stats
#
# ## Copyright Notice
#
# Copyright (C) 2019 The Connectome Coordination Facility (CCF)
#
# ## Author(s)
#
# * Timothy B. Brown, Neuroinformatics Research Group, Washington University in St. Louis
#
# ## Pr... |
53d8ff940588eec37fe39fe817f622f5f096875eb799bb65e3a251fcdd8c38f7 | Shell | 3,011 | 130 | #!/usr/bin/env bash
set -euo pipefail
BIDS_DIR=""
OUT_DIR=""
usage() {
echo "Usage: bash collect_baseline_mni_masks.sh --bids_dir /path/to/BIDS --out_dir /path/to/output"
exit 1
}
while [[ $# -gt 0 ]]; do
case "$1" in
--bids_dir)
BIDS_DIR="$2"
shift 2
;;
... |
3aaff8b38e67227c1251f1740fe1e26a4ce8af73fa6778f486c1ad2d2777177a | Shell | 3,018 | 71 | #!/bin/bash
source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@" # Debugging functions; also sources log.shlib
scriptName="basic_preproc_norm_intensity.sh"
echo -e "\n START: ${scriptName}"
workingdir=$1
b0maxbval=$2
echo "${scriptName}: Input Parameter: workingdir: ${workingdir}"
echo "${scriptName}: Input Paramet... |
0821750aa058b92968c93f8923e35c202aee5835e9479acab0022f4c2d44c682 | Shell | 3,053 | 55 | cwd="." # Change to working directory
cd $cwd
PATH_TO_SYRI="../syri/bin/syri" #Change the path to point to syri
## Get Yeast Reference genome
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/146/045/GCA_000146045.2_R64/GCA_000146045.2_R64_genomic.fna.gz
gzip -df GCA_000146045.2_R64_genomic.fna.gz
## Get Query g... |
83ff11e81167b4c80355315cbfd36cb40dced53ecc3af87bbbf9c47048a76dcd | Shell | 3,070 | 205 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}/cli.log"
mkdir -p "$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}"... |
fe5fc25ee1cbb3e0ce80cd8e766ae6f29ef6b1e29859a5e58f8cebc07dc78619 | Shell | 3,070 | 70 | #! /bin/bash
# RestorePreFreeSurferResamplingNHP.sh
# restore PreFreeSurfer resampling for NHP
set -eu
Usage () {
echo "Restore PreFreeSurfer resampling for NHP"
echo "$0 <StudyFolder> <Subject>"
exit 1;
}
[[ -z "${2:-}" ]] && Usage
# ------------------------------------------------------------------------------
# ... |
1cb32eb77387f1f92f2053069d26aaa50d263e64bd5ddba6f32af7375da3a8ec | Shell | 3,082 | 97 | #!/bin/bash
# Use recon-all output to generate WM mask in DWI space
# generate_wm_from_fs.sh --fs_output <FREESURFER_OUTPUT_DIR> --fs_to_dwi <FS_TO_DWI_TRANSFORM> --output_dir <OUTPUT_DIR> --dwi <DWI_IMAGE> --exclude [MASK1 MASK2 ...]
usage() {
echo "Usage: $0 --fs_output <FREESURFER_OUTPUT_DIR> --fs_to_dwi <FS_T... |
cb5f0d7b48b4aa66e23ab808e53a1a1cc9d3bb060251c619df3dcb451ec124d3 | Shell | 3,114 | 121 | #!/bin/bash
# file: preprocess-imagenet.sh
# auhtor: Andrea Vedaldi
# Use as:
# preprocess-imagenet.sh SRC_PATH DEST_PATH
#
# The script creates a copy of the ImageNet ILSVRC CLS-LOC challenge
# data while rescaling the images. Images are rescaled to a minimum
# side of 256 pixels. The data is supposed to be in the ... |
82d69afc86cd9e1f3f8de8c9c1117136adbc0b4779199ff9a678d01290da4141 | Shell | 3,122 | 89 | #!/bin/bash
# fsf_list=(/Users/boo/Desktop/fmri_script/fc_analysis/rois/roi_1*)
#
# for i in "${fsf_list[@]}"; do
#
# # #################################################
# # # stand2fun roi maker
# # # flirt -ref -in -out -init .mat -applyxfm
# # #################################################
# #/Users/boo/D... |
9c5a0236c59d3108befe7bf0c40434c24fff15c286d43ebcdda3856969d6413d | Shell | 3,127 | 164 | #!/bin/sh
#
# Downloads sequence for the hg19 version of H. spiens (human) from
# UCSC.
#
# Note that UCSC's hg19 build has three categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_gl??????_random.fa.gz
# 3. The alternative-haplotype files, na... |
8d2c4072c749bd5b763c2d3449fce3cee525c09414cd70bceda6d93bb4028293 | Shell | 3,131 | 109 | #!/usr/bin/env bash
#
# PRS-CS genome-wide polygenic score calculation script
# Usage:
# bash run_PRScs.sh <sumstats> <bim_prefix> <trait> <N_GWAS> <phi> <out_dir>
#
# Example:
# bash run_PRScs.sh \
# /path/to/ldblk_ukbb_eur.ASD.tsv \
# /path/to/genotype_prefix \
# ASD \
# 58948 \
# 1e-2 \
# ... |
146187c008da2358c05f67e89cd14b9d6c343bc5ca0b75ce5bb30cbf981f014a | Shell | 3,137 | 77 | #!/bin/bash -e
# Copyright (C) 2004-2011 University of Oxford
#
# SHCOPYRIGHT
Usage() {
echo ""
echo "Usage: mcflirt_acc <4dinput> <4doutput> [ref_image]"
echo ""
exit
}
[ "$2" = "" ] && Usage
input=`${FSLDIR}/bin/remove_ext ${1}`
output=`${FSLDIR}/bin/remove_ext ${2}`
TR=`fslval $input pixdim4`... |
d44a92b4c7ac60829986e352b35c70ce4c0a5b85b01eba8dfb61c474862acab5 | Shell | 3,184 | 63 | ############## TEN TUSCHER 2006 ##############################
MODEL_FILE_CPU="ten_tusscher_2006_RS_CPU.c"
MODEL_FILE_GPU="ten_tusscher_2006_RS_GPU.cu"
COMMON_HEADERS="ten_tusscher_2006.h"
COMPILE_MODEL_LIB "ten_tusscher_2006" "$MODEL_FILE_CPU" "$MODEL_FILE_GPU" "$COMMON_HEADERS"
#####################################... |
8833476d72e64b9ee65f0a35454e096bf0150480bf481eaf369ab7fe576b00b7 | Shell | 3,186 | 98 | #!/bin/bash
set -eu
# Function description
#
# For the given subject, identify_timepoins creates a string listing @ separated visits/timepoints to process
# Uses StudyFolder, ExcludeVisits, PossibleVisits global variables as input.
# Subject must be supplied as the first argument.
function identify_timepoints
{
... |
3609723d0adcf11cbce211ca3f6e30f17c5d92b2ddf6d499318c90c68a1a0b22 | Shell | 3,218 | 62 | # analyzes attribution scores (shap/saliency) for a set of DeepSTARR models trained w/ EvoAug
# can set DOWNSAMPLE and DISTILLED boolean variables
DOWNSAMPLED=true # toggle true/false
DISTILLED=true # toggle true/false
METHOD=saliency # set saliency/shap
FILES_DIR=../results/DeepSTARR_evoaug
if [ "$DOWNSAMPLED" = t... |
058beefa1b83526a74f45b4082aba676bd5f5b557b9c46458c2d3b93ec86099c | Shell | 3,220 | 104 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
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=... |
b3c1802c07c68603caf881836058b500eaef0862b02c2bbc3c227df9e4d6d17d | Shell | 3,220 | 100 | #!/bin/bash
set -e -E -u -o pipefail
RDscriptvalgrind ./.ci/install-r-deps.R --test || exit 1
sh build-cran-package.sh \
--r-executable=RDvalgrind \
--no-build-vignettes \
|| exit 1
RDvalgrind CMD INSTALL --preclean --install-tests lightgbm_*.tar.gz || exit 1
cd R-package/tests
ALL_LOGS_FILE="out.log"
VALGRI... |
8f19dae5d4cfc5d10ae15ad412d137bf744c58a5386ff245b46e2be341711b42 | Shell | 3,223 | 84 | #! /bin/bash
# brief: Import FCN models from Caffe Model Zoo
# author: Karel Lenc and Andrea Vedaldi
# Models are written to <MATCONVNET>/data/models
# You can delete <MATCONVNET>/data/tmp after conversion
# TODO apply patch to prototxt which will resize the outputs of cls layers from 205 -> 1000 (maybe sed?)
overwr... |
12e9c28ee67b52b96b0ef6674641bb0d6bef8c6e146d6c951bb098d94b4ce77e | Shell | 3,248 | 88 | #!/bin/sh
#============================================================
# iso2mesh inline documentation to wiki convertor
#
# Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
#============================================================
print_help()
{
awk '/^%/ {dp=1} /-- this function is part of iso2mesh/ {... |
77daaa856bc549fe4f78709040fcf94cc631de17eb9f38562ba636c05023d2f9 | Shell | 3,265 | 116 | #!/bin/bash
#
# Usage: sh_md5alldir.sh [OPTIONS] </path/to/dir/>
#
##############################################################
## Description ##
##############################################################
#
# This script will process all sub-directories of the input fo... |
1bb475b5370eebf323124e3bbadb317a4c6075717490cdb28bf5c783461ac77f | Shell | 3,274 | 83 | #!/bin/bash
# Chante Bethell for CCDL 2020
#
# Run the HGG molecular subtyping pipeline.
# Note: A local install of BEDOPS is required and can be installed using
# conda install -c bioconda bedops
# When OPENPBTA_SUBSET=1 (default), new HGG subset files will be generated.
set -e
set -o pipefail
# This option control... |
79fbb5664f390641792cbd8b8e0a205108ce29fd536bca25951ab1de8c388d97 | Shell | 3,274 | 72 | # run ensemble_predict_DeepSTARR.py with both --distill and --eval flags set
# toggle DOWNSAMPLED to control whether distilled training data is obtained for downsampled models
DOWNSAMPLED=true # toggle true/false
# MODEL_DIR=../results/DeepSTARR_lr-decay/sanity_check
MODEL_DIR=../results/DeepSTARR_ensemble_NEW # path ... |
06ae34a88ee2bc0be2adbebcf62d60143c637034ded35182d63bdff036171b40 | Shell | 3,288 | 50 |
if [ -n "$CUDA_FOUND" ]; then
TEST_OPT_DEPS=gpu_utils
fi
TESTS_DYNAMIC_DEPS="$CUDA_LIBRARIES $CRITERION_LIBRARIES dl m logger ${TEST_OPT_DEPS}"
if [ -n "$AMGX_FOUND" ]; then
TESTS_DYNAMIC_DEPS="$TESTS_DYNAMIC_DEPS $AMGX_LIBRARIES"
fi
##Tests
TESTS_STATIC_DEPS="monodomain ode_solver config tinyexpr config_he... |
b70ba72058c2839486bf13ef4006b4c8593a2b883620a5422154e22e326b4143 | Shell | 3,292 | 116 | #!/bin/bash
#
# Usage: sh_sha1alldir.sh [OPTIONS] </path/to/dir/>
#
##############################################################
## Description ##
##############################################################
#
# This script will process all sub-directories of the input f... |
883ab7ff03771583f8f80c0756db7b537706b76e2681408bcb58ceb1d458f657 | Shell | 3,303 | 77 | #!/bin/bash
# normalize multiple QSM images (native space) to MNI space using command-line arguments
# Required arguments:
# --t1w <T1w image>
# --qsm2t1w_xfm <QSM to T1w transformation matrix>
# --output <Output directory>
# --anat <FSL_ANAT directory>
# --input <One or more QSM images>
usage() {
echo "Usage: $0... |
500d377f53e6e7277b62fe0ecb8b48de23cd96b710c5983b519e97197181c0be | Shell | 3,310 | 105 | #!/bin/bash
# 1 {input.ncbi2ucsc}
# 2 {input.ucsc2ncbi}
# 3 {input.vcf_file}
# 4 {input.bam_file}
# 5 {wildcards.vcf}--{wildcards.rna}
# 6 {input.fasta}
# 7 {config[mae][gatkIgnoreHeaderCheck]}
# 8 {output.counted}
# 9 {params.bcftools}
#10 {params.samtools}
#11 {params.gatk}
#12 {threads}
ncbi2ucsc=$1
ucsc2ncbi=$2
v... |
1b2d9d3550483e3fa5a68ee0e64c73a2dfc786867ccbb15fba17d5aaa8df0384 | Shell | 3,320 | 67 | #!/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... |
60ac8a58315c5c98d3dc6f43a7edb74482e6c851a81ded37f7055db83e5918f4 | Shell | 3,338 | 121 | #!/usr/bin/env bash
set -euo pipefail
wm_mask="$1"
tck_file="$2"
out_tract_mask="$3"
out_tdi_norm="$4"
out_wm_mask="$5"
# make a temp dir
tmpdir="$(mktemp -d)"
cleanup() { rm -rf "$tmpdir"; }
trap cleanup EXIT
# ----------------------------
# Basic input checks
# ----------------------------
if [[ ! -f "$wm_mask" ]... |
3c25f43a1cdc9b483d67b4c02ea46579bc09127f9eba2eac4f9f85a17213ef60 | Shell | 3,350 | 90 | #!/bin/bash
#SBATCH --job-name=biopathnet_biomed_mock_perturbations
#SBATCH --output=/lustre/groups/crna01/projects/synthetic_lethality/BioPathNet/slurm_out/run_mock_perturbations.txt
#SBATCH --error=/lustre/groups/crna01/projects/synthetic_lethality/BioPathNet/slurm_out/run_mock_perturbations.err
#SBATCH --time=01:00:... |
4fa645a4fae7fe0c80c4d615da4b5a37392bae7c7f9bd568fd15c0f33cbb6b4b | Shell | 3,370 | 130 | #!/usr/bin/env bash
# the next line restart using vmd \
exec vmd "-dispdev text -e $0"
set NRES 6
################################################################################
# #
# Generate the index file for calculating the Phi/Psi a... |
6f38edc040e4967d34e42d5d649cb485724ff88a437adfb184573e38826c19e9 | Shell | 3,373 | 116 | #!/bin/bash
# JA Shapiro for CCDL 2019-2020
#
# Runs scripts/01-process_mutations.R with some default settings.
# Takes one enviroment variable, `OPENPBTA_ALL`, which if 0 runs only
# the full dataset and the largest disease set (for testing). If 1 or more,
# all samples ar run (this is also the default behavior if un... |
660c732e962cf749d56e1eaadf0be60d10453ca68ea2b2fa60795241ba9f0a35 | Shell | 3,380 | 119 | #!/bin/bash
set -eu
pipedirguessed=0
if [[ "${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" "$@"
opts... |
09216ad745b205e5d68660835eddd7c14317eafaf261fa5acbcaf53bf0628520 | Shell | 3,410 | 85 | #!/bin/bash
SCRIPTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
WEBSITE_S3=kuceyeski-wcm-web
NEMODATA_S3=kuceyeski-wcm-nemodata
BACKUP_TIMESTAMP=$(date +"%Y%m%d_%H%M%S")
WEBSITE_S3_BACKUP_DIR=${WEBSITE_S3}/nemo_website_backups/backup_${BACKUP_TIMESTAMP}
function backup_and_upload {
loc... |
75fbaf1b3506bb17bf801a527be6b1db4b65ec3cbec9898715e4befb187a8b17 | Shell | 3,412 | 106 | #!/bin/bash
set -e
# 1 {input.ncbi2ucsc}
# 2 {input.ucsc2ncbi}
# 3 {input.vcf_file}
# 4 {wildcards.vcf}
# 5 {input.bam_file}
# 6 {output.snvs_filename}
# 7 {config[tools][bcftoolsCmd]}
# 8 {config[tools][samtoolsCmd]}
ncbi2ucsc=$1
ucsc2ncbi=$2
vcf_file=$3
vcf_id=$4
bam_file=$5
output=$6
bcftools=$7
samtools=$8
tmp=$... |
b8acadbc75cd44dfcbe85d75424c16725dfc83aee3848e46460dc3a3c99f4f1b | Shell | 3,421 | 67 | #!/bin/bash
# R. Corbett (adapted from J. Taroni for ALSF CCDL)
# December 2022
set -e
set -o pipefail
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# In CI we'll run an abbreviated version of the de novo signatures extraction
ABBREVIATED_MUTSIGS=${OPC_QUICK_MUTSIGS:... |
8b53b7b927ffa7ad5ed2a8c17c31ebf3dcd76e773ffde37416b1ee49396bea6a | Shell | 3,461 | 75 | #!/bin/sh
# You do not want to run this. It was used to create the initial repo by
# extracting the relevant bits from Canu and renaming things.
if [ `pwd` != "/scratch/git/canu-test" ] ; then
echo Wrong directory.
exit
fi
echo DELETE
rm -rf .git *
echo SYNC
rsync -a ../canu-orig/ .
echo REWRITE
../git-filt... |
f8620771df5de9beadc5d7eb716e421bcd5f56dd2963d32df7bad0fbf656a2ae | Shell | 3,476 | 91 | #!/bin/bash
# PediatricOpenTargets 2021
# Yuanchao Zhang
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
# copied from the run_in_ci.sh file at
# <https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/scripts/>
script_directory="$(perl -e 'us... |
5e08c9e51c7590407384b068985e018ec12be1e1c88be2f97cd7c9da88d49da7 | Shell | 3,481 | 97 | #!/bin/sh
# You do not want to run this. It was used to create the initial repo by
# extracting the relevant bits from Canu/Meryl and renaming things.
if [ `pwd` != "/scratch/git/meryl-filtered" ] ; then
echo Wrong directory.
exit
fi
echo DELETE
rm -rf .git *
echo SYNC
rsync -a ../meryl-orig/ .
echo REWRITE... |
a8598eea287e38f9e1d1429ba506973fa1a8d6df366a9b7b29f97278ca01680e | Shell | 3,490 | 185 | #!/bin/sh
#
# Create BEM surfaces using the watershed algoritm included with
# FreeSurfer
#
# Copyright 2006
#
# Matti Hamalainen
# Athinoula A. Martinos Center for Biomedical Imaging
# Massachusetts General Hospital
# Charlestown, MA, USA
#
# $Header: /space/orsay/8/users/msh/... |
91b9be01bfc69727d185d30a019574881ad300bdf53ff0334418b63323b694af | Shell | 3,492 | 82 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
864c0b0826854bdc72a85d170549b64b ${pref}_m15_s2M.histo
864c0b0826854bdc72a85d170549b64b ${pref}_m15_s16M.histo
41fd8408dde0ea14bec7425b1a877140 ${pref}_m15.stats
376761a6e273b57b3428c14e3b536edf ${pref}_binary.dump
376761a6e273b57b3428c14e3b536edf $... |
46c17ac581f98a40e0a8a3f4c79411c48ffc6f9a298827d65e6d156aefbbff26 | Shell | 3,499 | 106 | #!/bin/bash -l
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-gpu=40gb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --partition=gpuq
#SBATCH --time=00-23:59:59
#SBATCH --output=job_default.out
# Function to parse named arguments
parse_args() {
while [[ "$#" -gt 0 ]]; do
case $1 i... |
a5bfba3659000a83f0df82d75627c14e123c521e094561bde460d11061d92325 | Shell | 3,504 | 135 | #!/bin/bash
FIND_CUDA () {
#CUDA RELATED VARIABLES
CUDA_LIBRARY_PATH=""
CUDA_MATH_LIBRARY_PATH=""
CUDA_INCLUDE_PATH=""
NVCC=""
CUDA_FOUND=""
LD_CONFIG=ldconfig
if [ "$OS" == "openSUSE Tumbleweed" ]; then
LD_CONFIG=/sbin/ldconfig
fi
if [ -z "$CUDA_LIBRARY_PATH" ]; then
CUDA_LIBRARY_PATH=$(dirname "$($L... |
a458635bd18914bb4ce1e6394d61f8d418109d39d384ad2da14bf098c97fa27f | Shell | 3,507 | 107 | #!/bin/bash
# Script for checking license at begin of files for bash.
# Run with:
# chmod u+x check_for_license.sh
# ./check_for_license.sh
# Change directory to the root of the Git repository
cd "$(git rev-parse --show-cdup)"
# Ignore list (directories or subdirectories to ignore)
ignore_list=("cpp/memilio/ad" "... |
6d90b66862dd3750ac58b2918d582dc5636169a1d7b6b99c946ac237b6caa35c | Shell | 3,517 | 107 | #!/bin/sh
#
# Downloads sequence for H. sapiens (human) from NCBI.
#
# A relatively new directory structure (as of Oct 2011) seems to have collected
# all the relevant files in one directory (MT no longer separate) and
# eliminated the alternative haplotype assembles from the main directory
#
# It's generally a good i... |
86bdc1613d4b590abeb14b54b92a403da8b0238b89fdf660a9aa449c7d23e000 | Shell | 3,526 | 75 | #!/bin/bash
#-----------------------------------------------------------------------------#
# AFNI surface clustering for NumpRF tuning parameter maps (fsaverage)
# AFNI <full_path_to_this_script> <sub> <ses> <model> <img> <anat>
#
# <full_path_to_this_script>
# = /data/hu_soch/ownCloud/MPI/EMPRISE/too... |
44e23f9e7bc3bef047764eaa7cac5f4233af7f69ec9ab3724d823ecc577274df | Shell | 3,555 | 89 | #!/bin/bash
# Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... |
9f49b6d7450a5196047c32afd9c4051b224eb1edcd0ba2c6fa7bd419cfe363dc | Shell | 3,574 | 73 | #!/usr/bin/env bash
#set -e
bids_dir=$1
subject_id=$2
session_id=$3
qsirecon_dsistudio_dir=$bids_dir/derivatives/qsirecon-DSIStudio/sub-${subject_id}/ses-${session_id}/dwi
# Search for *space-ACPC_model-gqi_dwimap.fib.gz
fib_file=$(find $qsirecon_dsistudio_dir -type f -name "*space-ACPC_connectivity.mat" | head -n 1... |
e197657443d4952f5504e276efe08bb00d4c8694bf2179068a468e2736069c45 | Shell | 3,574 | 129 | #!/bin/bash
#
# [description]
# Helper script for checking versions in the dynamic symbol table.
# This script checks that LightGBM library is linked to the appropriate symbol versions.
# Linking to newer symbol versions at compile time is problematic because it could result
# in built artifacts being u... |
03387b0782446c3872378c139376120aa9ad16d43123b3dbfe415ebd77412080 | Shell | 3,580 | 99 | #! /bin/bash
# brief: Import Fast R-CNN models
# author: Abhishek Dutta
# author: Hakan Bilen
# Models are written to <MATCONVNET>/data/models-import/fast-rcnn
# You can delete <MATCONVNET>/data/models-import/fast-rcnn/fast_rcnn_models.tgz
# TODO apply patch to prototxt which will resize the outputs of cls layers fro... |
08c9a1a6fb1c178b5a355fd52b068a30f672d5b762197dc4e75c2269d5402013 | Shell | 3,585 | 126 | #!/bin/sh
set -e
set -o pipefail
printf "Start molecular subtyping...\n\n"
# Set locations for s3 bucket that contains release file
URL="s3://d3b-openaccess-us-east-1-prd-pbta/open-targets"
RELEASE="v14"
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# Get base direct... |
49ab472e0aec787becf3ffd1820b0ac1f8b7f41ca067494185b9db9257bb754e | Shell | 3,589 | 123 | #!/usr/bin/env bash
set -euo pipefail
xfm_root="/mnt/f/BIDS/WCH_AF_Project/derivatives/xfm"
qsiprep_root="/mnt/f/BIDS/WCH_AF_Project/derivatives/qsiprep"
dwi_root="/mnt/f/BIDS/WCH_AF_Project/derivatives/dwi_pipeline"
out_root="/mnt/e/Neuroimage/workdir/TBSS_GBSS"
gm_out_dir="$out_root/GM_fraction"
tmp_root="$out_root... |
ca39098693489c4f573d8ab4e507f1e9b9bc1c5d26b86f24643f0c1da8a41ca3 | Shell | 3,591 | 93 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Andreas Schuh
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Ap... |
9988b25d452883d74bfda0b1244864c70ee54cc7d2dacda5909f2d9e4ffdab08 | Shell | 3,598 | 111 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
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=... |
65eb45d70946fdd7dc57f8d7d02041e7f743b176631def72ca7cb16bb0fef9d6 | Shell | 3,611 | 70 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Apache License, Version 2.0 (the "Lice... |
001f3b5e114ba2397ae48cd9f7caeaae8238a419f04b8026a77acb74c696bc4a | Shell | 3,651 | 90 | # run ensemble_predict_MPRAnn.py with both --distill and --eval flags set
# runs ensemble_predict_MPRAnn.py in distill mode
# for MPRAnn ensemble trained on full training data
# toggle DOWNSAMPLED to control whether distilled training data is obtained for downsampled models
MODELS_DIR=../results/MPRAnn
N_MODS=10
DAT... |
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