sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
59af06d8afc423cfcacf5aed93caf9f406cdb957a35bc0ff5890e3a3e1066df0 | Shell | 21,037 | 619 | #!/bin/bash
#: Title : test_simframe
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../simframe
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
fbbbc22b966db2ba354f39a3a95265668e08d3d24af85c02ce5f7218a97ec2ca | Shell | 21,077 | 603 | #!/bin/bash
#: Title : test_imgbfbp
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgbfbp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
21faac106c93bb1187dd9dfbf180de8f713f0f9bfe41b439296886a7e8fbe2fd | Shell | 21,144 | 542 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=10:00:00
#SBATCH --job-name=dask-root
#SBATCH --mem=30GB
#SBATCH --signal=B:SIGUSR1@120
#SBATCH --mail-type=end
#SBATCH --mail-type=fail
#SBATCH --mail-type=begin
#SBATCH --output=job.%j.log
#SBATCH --error=job.%j.err
# start ti... |
bb6686d8b4a05dc97e9b9b67b993c772452c101fc54208ade40add1c67bfdd6f | Shell | 21,216 | 634 | #!/bin/bash
#: Title : test_imgsrtm
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgsrtm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
df7d8135e5a149bf6d2139db59fdd498844238f33e9606095ff57c672c5dce6f | Shell | 21,511 | 518 | #!/bin/bash
#: Title : test_maskeros
#: Date : 2019-11-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../maskeros
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
4e91444b5b46cfac6df8432d396ab1639dd1d069c390a4730892b5b92432d2a5 | Shell | 21,543 | 546 | #!/bin/bash
#: Title : test_llsqrk2
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../llsqrk2
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
95921b40370d03e97c9405c258772e71d23c3f1e92f200108d9a778734d47f51 | Shell | 21,933 | 681 | #!/bin/bash
#: Title : test_ecat2ana
#: Date : 2026-09-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ecat2ana
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
7eebe425782a1a5f34b1cc0e134294dacfe5433ad61a1e29e12ea6acac716076 | Shell | 22,342 | 704 | #!/bin/bash
#: Title : test_imgcalc
#: Date : 2018-02-25
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgcalc
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
39bc08c6f4be2ffa785b40ad0166cbfa4524e803c105bcdde9291834389a8961 | Shell | 22,429 | 640 | #!/bin/bash
#: Title : test_parmatch
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../parmatch
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
80293e868798b18e7844c370db6da1fd5573e615c6ead2486566429c08a81567 | Shell | 22,629 | 477 | #!/bin/bash
#
# Registers T1w --> dwi space using a nonlinear SyN method for a given SUBJECT & SES
# Uses a combo wm-gm FOD as a fixed image in the reg
# Focuses on solving the excessive cortical expansion observed in some subjects e.g., 08 & 11
#
# # INPUTS:
# $1 : id = num in (01..30)
# $2 : SES = num in 1, 2... |
0bb967a7f461ba74e362fa69057107d77ead461f2de77fc144be8c4965bb9100 | Shell | 22,870 | 604 | #!/bin/bash
#: Title : test_p2t_v3c
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../p2t_v3c
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
4d8efc4a48dc5b99b261422815610e3d5c05b91fac5f2c6c7c448e87c9476a8a | Shell | 23,195 | 791 | #!/bin/bash
#: Title : test_taccalc
#: Date : 2026-05-11
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../taccalc
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
5485935aa4fced6975b9178f81df3d9b745450178848172a8c67b08ccd6567d3 | Shell | 23,360 | 641 | #!/bin/bash
#: Title : test_fit_sinf
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_sinf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
04fd6b4611d09c0d17b07a9b1dd0b76ca29ebf3f0a67f33b8717005f21e7227a | Shell | 23,490 | 285 | python train.py --name ResNet_l1 --dataset roman-empire --model ResNet --num_layers 1 --device cuda:0
python train.py --name ResNet_l2 --dataset roman-empire --model ResNet --num_layers 2 --device cuda:0
python train.py --name ResNet_l3 --dataset roman-empire --model ResNet --num_layers 3 --device cuda:0
python train.p... |
2160dbb6d787ae6bbf4ca548f98b2b5378b331866955a3b75b41a1a27257b5dd | Shell | 23,723 | 563 | #!/bin/bash
#: Title : test_maskdila
#: Date : 2019-11-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../maskdila
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
87e43d2d17d0af49c00f7ee49b8eddd078cd23d4dda1da1c5cb3d9896b4c7c0c | Shell | 24,046 | 579 | #!/bin/bash
#: Title : test_fitk2di
#: Date : 2023-06-30
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitk2di
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
d47bc7af13a479bf811a79a541d65ea58c73dcf0cef8f49274cf95bdae89ce41 | Shell | 24,131 | 678 | #!/bin/bash
#: Title : test_metabcor
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../metabcor
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
75a403952b3ecbcc33b249896b24139a7e042e1d3a9fb7b62842edf7ac793290 | Shell | 24,872 | 671 | #!/bin/bash
#: Title : test_imgfur
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgfur
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
94e8434cfd19b93564b3c240b983aaa8c8e01f2d789a9df8d7942ef740f724f2 | Shell | 25,156 | 696 | #!/bin/bash
#: Title : test_tactime
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tactime
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
f95cd5d8cf710f7bbc3bd4f94b25fcf731c2090000e7810981a344a7241191b3 | Shell | 25,277 | 753 | #!/bin/bash
#: Title : test_absstime
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../absstime
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
4cadae3e07b821c75988c2a474590eaa84ea2d1d33139fbdd6b804c633729f98 | Shell | 25,651 | 532 | #check the help info for step 1
#Rscript step1_fitNULLGLMM.R --help
#For Binary traits
#For single-variant association tests.
#Not use sparse GRM and not use categorical variance ratios#
#randomly selected markers with MAC >= 20 in the plink file are used to estimate the variance ratio
#--minMAFforGRM can be used fo... |
630727532a980f161a3be42919e41262e3eb66c06ae90cda3baf92865cf57cdc | Shell | 25,659 | 641 | #!/bin/bash
#: Title : test_imgbfh2om
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgbfh2om
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist... |
777b70b051e7151e52ddee1183b345e5eb12b9b144cd248bf8693539d246e656 | Shell | 25,745 | 533 | #check the help info for step 1
#Rscript step1_fitNULLGLMM.R --help
#For Binary traits
#For single-variant association tests.
#Not use sparse GRM and not use categorical variance ratios#
#randomly selected markers with MAC >= 20 in the plink file are used to estimate the variance ratio
#--minMAFforGRM can be used fo... |
822c8f263464c0473c71b65fb7faf6c9892dfb02efc9843a45222bc7fbdeab2f | Shell | 25,753 | 651 | #!/bin/bash
#: Title : test_imgbfh2o
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgbfh2o
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
6579210a3832d4f9f37198a8ad2a86176f476247c21156ad621870678e317ecc | Shell | 25,832 | 687 | #!/bin/bash
#: Title : test_p2t_3c
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../p2t_3c
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
d26bb0c8507b2e893fa5f6274f65951714759192fe0af58a0d84cd2266f22809 | Shell | 26,022 | 705 | #!/bin/bash
#: Title : test_fitk4di
#: Date : 2024-06-19
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitk4di
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
9cd9e2571c7222c3f423ca5a931450e016ae1c69f01935d56f79e27e12b306c5 | Shell | 26,278 | 780 | #!/bin/bash
#: Title : test_fit_sigm
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_sigm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
a0f9f69f8c255273478bc40ec4525f1ef4fd2fdbb529aff910e697a6d8af2caf | Shell | 26,420 | 663 | #!/bin/bash
#: Title : test_imgdv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgdv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
8c3233173d33ad2eefe7bd79a8ca2fb4fe23231569d5f7919459967a2b166637 | Shell | 26,616 | 773 | #!/bin/bash
#: Title : test_resmatch
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../resmatch
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
37880232c72a3e1a6ad09dcc559e680b01cf66e6766ff623bd3a281589db4e75 | Shell | 26,706 | 290 | #!/bin/bash
# This script is adjusted from HCP's FS2CaretConvertRegisterNonlinear
# script, and creates sets of cortical meshes at various resolutions,
# which are surface-registered to a template, and which can be directly
# used for group-level averaging. The results will be stored in the
# directory 'workbench', i... |
db2338b4550415610d946f33bc1aae1000577db63fc72428de3479bfb48176d2 | Shell | 26,751 | 686 | #!/bin/bash
# test_gsn_matlab_python_equivalence.sh
#
# This script tests numeric equivalence between Python and MATLAB implementations
# of GSN (perform_gsn / performgsn) using simulated data.
#
# Strategy:
# 1. Generate test data once in Python (with deterministic seed) and save as
# both .npy and .mat so Pyt... |
f0fe4a9cada07943cda6208e615d0b5e69decf7a050fd567e53fa0e473aa94c5 | Shell | 26,907 | 906 | #!/bin/bash
#: Title : test_taccat
#: Date : 2024-06-18
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../taccat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
97fd3ad50eb1dbd5e56667cbdd958b5864c5528ba57a483b437136bf9181439e | Shell | 26,925 | 164 | PARTITION=$1
WORK_DIR=$2
CPUS_PER_TASK=${3:-4}
echo 'configs/albu_example/mask-rcnn_r50_fpn_albu_1x_coco.py' &
GPUS=8 GPUS_PER_NODE=8 CPUS_PER_TASK=$CPUS_PRE_TASK ./tools/slurm_train.sh $PARTITION mask-rcnn_r50_fpn_albu_1x_coco configs/albu_example/mask-rcnn_r50_fpn_albu_1x_coco.py $WORK_DIR/mask-rcnn_r50_fpn_albu_1... |
fbd9d03022de091fc9475aee913828f460c75b476306e4ee277591263187e744 | Shell | 27,684 | 738 | #!/bin/bash
#: Title : test_regfur
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../regfur
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
0bada95f8b8dd184dee4cbdad1d596834afcba7f2360b13e92fc11474c047c8e | Shell | 27,827 | 584 | #!/bin/bash
# update script on the GBiB virtual machine
# - updates itself and then run itself
# - updates cgis, html and gbdb via rsync
# - patches the menu
# - calls hgMirror to hide some slow default tracks, e.g. conservation+retro
# will not run if:
# - not run as root
# - if a script named updateBrowser.sh alr... |
2fc13837ef07e86b9124c79852a816cdfa57bcf4dbf1f7a1cda816ca2f64cd92 | Shell | 28,502 | 756 | #!/bin/bash
#: Title : test_fitk3
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitk3
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
541d3f534bf491ef157d8ab06b19ef7fad9e12fab64bbd94289d4854ab6eddd2 | Shell | 28,678 | 622 | #!/bin/bash
#
# A Test script which registers T1w & dwi images using ANTS to facilitate fine tuning of the registration method
#
# NOTE: FUNCTION IS NOT MEANT TO BE CALLED,
# CURRENTLY THIS CODE IS BEING DEVELOPED AND TESTED MANUALLY.
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-------------... |
3f9f24f6d4ce84c3f6c01ba55947b59acb7252b2c95e99a1c8560b788ecbadc7 | Shell | 28,682 | 894 | #!/bin/bash
#: Title : test_flat2img
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../flat2img
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
966dc8d07e0f3f42b01476d363d1204a75a2d27f91dcb5236908076369b357c8 | Shell | 28,880 | 777 | #!/bin/bash
#: Title : test_fitk5
#: Date : 2019-08-26
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitk5
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
615276ef421b2ea7e18964a246f2b1023bc2463a72592c2e73de51aeec741be6 | Shell | 29,199 | 899 | #!/bin/bash
#: Title : test_imgdecay
#: Date : 2026-09-13
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgdecay
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
190c36b8bb0119bbab775789938c616dbfca58d8c0a2deb12d39c673a8b6c9ee | Shell | 30,147 | 861 | #!/bin/bash
#: Title : test_absscal
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../absscal
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
63c9efadb0734468116e6ce4903b6521cc97d0f922c60f13bbf83022b594d472 | Shell | 30,645 | 919 | #!/bin/bash
#: Title : test_imginteg
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imginteg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
16dc11a60b4678ba06c9b1018f0fbb2e92ba8d406ff270fddfe2bd599236852d | Shell | 30,670 | 794 | #!/bin/bash
#: Title : test_imgflow
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgflow
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
5bbf674d768d025028c733a5d74da883235c9762e54b8f39765cc8133cac23c7 | Shell | 30,778 | 610 | #!/bin/bash
#
# Registers T1w <--> FUNC space using a nonlinear SyN method for a given SUBJECT & SES
#
# NOTE: specifically targeting problematic subjects: 08 11 13 18 18r 19 20 21r 26 27
#
# RESULTS FROM EACH STAGE:
#
# 1. MI-AffineOnly : Large shrinkage of cortical surface
# 2. CC-AffineOnly : Better regist... |
36a729875c48d377438e0f9783f2704077c730438950577e9426c0e2c8db6628 | Shell | 30,779 | 157 | PARTITION=$1
CHECKPOINT_DIR=$2
WORK_DIR=$3
CPUS_PER_TASK=${4:-2}
echo 'configs/atss/atss_r50_fpn_1x_coco.py' &
GPUS=8 GPUS_PER_NODE=8 CPUS_PER_TASK=$CPUS_PRE_TASK tools/slurm_test.sh $PARTITION atss_r50_fpn_1x_coco configs/atss/atss_r50_fpn_1x_coco.py $CHECKPOINT_DIR/atss_r50_fpn_1x_coco_20200209-985f7bd0.pth --work... |
137dfdcf92a840b8b12b64795502a3dc63afa39e0555bb659e59ff987c50c277 | Shell | 30,994 | 794 | #!/bin/bash
#: Title : test_fitk2
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitk2
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
bc6d04ae7b4f2c0e7e80b74f15bbbfb5be0341adf7a2aa8e5b3d9608df3a4642 | Shell | 32,687 | 876 | #!/bin/bash
#: Title : test_fitk4
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitk4
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
347bf27b22c7fa13ff7ccff89095902a467e65f0d7eafe0fb90383416c02ed3b | Shell | 34,012 | 732 | #!/bin/bash
#
# MINIMAL VERSION FOCUSED ON MODIFYING THE SURFACE-BASED REGISTRATIONS
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 : participant
# $3 : Out Directory
#
BIDS=$1
id=$2
out=$3
SES=$4
nocleanup=$5
threads=$6
tmpDir=$7
changeTopupConfig=$8
changeIcaFixTraining=$9
thisMainScan=${10}
thisPhase=${11}
... |
6ca014ebb9fb95cc5da1084acd32122ff97a7d9393740b43fa5bab17132a9cd1 | Shell | 35,186 | 910 | #############################
# screen -r -D 124494.pts-46.login-p-1
# Sims:
# screen -r -D 167694.pts-0.login-p-2
# GPU
# real data:
# screen -r -D 10750.pts-51.login-e-2
# Sims
# screen -r -D 5125.pts-16.login-e-4
# scontrol show jobid -dd 36062877
# reusable functions and variables used by other scripts
######... |
7017da50384cf3b688f59fe5785feab6504a2a96dea6243426fc28d72ca062dd | Shell | 37,373 | 1,003 | #!/bin/bash
#
# MICA BIDS structural processing
#
# Utilities
export Version="v0.1.5 'Roadrunner'"
bids_variables() {
# This functions assignes variables names acording to:
# BIDS directory = $1
# participant ID = $2
# Out directory = $3
# session = $4
BIDS=$1
id=$2
out=$3
SES... |
62f107990e62a19df886696c1b0c79eee60776765158b406652165f50a7ac184 | Shell | 37,431 | 722 | #!/bin/bash
#
# DWI structural processing with bash:
#
# Preprocessing workflow for diffusion MRI.
#
# This workflow makes use of MRtrix3
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 : participant
# $3 : Out parcDir... |
df60b938c60909d01c9b9cff257582dfa49aca9ea22e2b61afcbb0760f82c45d | Shell | 37,753 | 616 | #!/bin/bash
#
# DWI POST structural TRACTOGRAPHY processing with bash:
#
# POST processing workflow for diffusion MRI TRACTOGRAPHY.
#
# This workflow makes use of MRtrix3
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 :... |
5bd7f5659979406c10d60bca2aafa2830d9cba90befeadce60c05f6d904deaa9 | Shell | 38,383 | 78 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
sbatch --array=0-255 -n 16 --tmp=10000 --time=24:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/Functional_Basis_set_screening_logs/Functional_Basis_set_... |
0af08746dba4467be6d1ccbe83a41b239236fc4dd18d27a879ccd6e1763131bb | Shell | 38,429 | 1,057 | #!/bin/bash
#: Title : test_imgfiltg
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgfiltg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
68757af2e42ff3ac8fab889851af25dbd6f740c55a5a56d4f2dceafbd6e7fa11 | Shell | 38,962 | 795 | Rscript step1_fitNULLGLMM_0.41.R --plinkFile=./input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly --phenoFile=./input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt --phenoCol=y_binary --covarColList=x1,x2 --sampleIDColinphenoFile=IID --traitType=bin... |
4b8a3567b24ccae7515d764e5ea9b84c8ea1242f4715184f0ddc919d78715b35 | Shell | 39,383 | 1,039 | #!/bin/bash
#: Title : test_pbconv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executables to test
PROGRAM1=../../b2plasma
if [ ! -f $PROGRAM1 ]; then
if [ ! -f $PROGRAM1.exe ]; then
printf "Failed: executable $PROGRAM1 does not exis... |
a3bd945861b1767695c8bd55a9d89676ef28f86f5d86a1839ba6c3cda58f6c18 | Shell | 39,589 | 881 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
set build hg19
set defaultdest /complgen/refseqnew
# settings
set genomeurl {}
set par {chromosome begin end name
X 60001 2699520 PAR1
X 154931044 155260560 PAR2
Y 10001 2649520 PAR1
Y 59034050 59363566 PAR2
}
set organelles {chromosome
chrM
}
... |
1eceb5b74c3fa19d1f92073befd370348ab13dd4635225173621837f38a5abf0 | Shell | 41,815 | 1,137 | #!/bin/bash
#: Title : test_fit_h2o
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_h2o
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6acd6a9f1885366a3f80d2266e88c8bf0d90f43c2e15d78efff9fa92611c7fcd | Shell | 42,020 | 982 | #!/bin/bash
#: Title : test_p2t_di
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../p2t_di
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
aaaf65001cff96041ee795b03ecbfc770e41b47e50ae4d7d4e305534dae9c7b4 | Shell | 42,879 | 1,178 | #!/bin/bash
#: Title : test_fit_feng
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the exit status of a pipeline to the exit status of failed, not the last command in the pipeline
set -o pipefail
# Set the name of executable to test
PROGRAM=../../fit_f... |
daf4ec89d03b82b031419d20c7ed0d685a5d155b3f2be60ad09e969e9ec41d60 | Shell | 43,188 | 804 |
# PRS GXE project simulations
#
#
#####################
source ~/pytorch-env113/bin/activate
########
# take the _smallcases genotype set, randomly subset to 500K SNPs
pheN="_smallcases"
mkdir -p $simsData
# from this pick a random $numControlsToPick number of indis
numSNPs=$(wc -l < $UKBB_PLINK1$'ALL_KEEP_T... |
f93f60a75e4a6721ee89177ac05c7455b1c5780950ed566a62da993b13eddce6 | Shell | 44,382 | 1,217 | #!/bin/bash
#: Title : test_sim_3tcm
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the exit status of a pipeline to the exit status of failed, not the last command in the pipeline
set -o pipefail
# Set the name of executable to test
PROGRAM=../../sim_... |
32cbe8e1195c2599fdedf19354d30992aee1d83f09336f52d1d03e5840b14a61 | Shell | 44,817 | 1,302 | #!/bin/bash
#: Title : test_fit_srtm
#: Date : 2022-03-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_srtm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
c02439bd177848a603ab7f5321109de80cc53505b01d61b4bdb7e0aeb11b79c3 | Shell | 50,714 | 1,197 | #!/bin/bash
#: Title : test_patlak
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../patlak
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
f0f5885af00147109ffc4d1ac6386f9070bb616148fd8336948b663ff34b42cf | Shell | 51,598 | 921 | #!/bin/bash
########################################################
# Author: Carrisa V. Cocuzza. 2023. Yale University. Holmes Lab.
# Description: Per participant, this script performs the main steps in fMRI data processing after HCP minimal preprocessing.
# NOTES:
# (1) This is set up for the TCP dataset and t... |
86f8674c67290c5db040aa05bdc1d5e433c924f87a82b936c3cbf38a3ee170ed | Shell | 52,466 | 1,031 | #!/bin/bash
# Resting state preprocessing
# Written by Casey Paquola and Reinder Vos De Wael (Oct 2018).
# and a tiny bit from Sara (Feb 2019)...
# and a whole lot from Sara (August 2019)
# and incorporation to mica-pipe by Raul (August-September 2020)
# and addition of a bunch of fancy flags by Jessica (October-Novemb... |
22d094b60b9b44ee06e831fbccb9157c80e6fec27f49cf3e3ef35780e27c2fb1 | Shell | 56,369 | 1,316 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
# Script to download and prepare all reference databases (including genome) for hg38
# call using
# makedbs_hg38.sh ?options? ?dest? ?webcache?
# where
# * dest: the directory where the reference databases will be installed (default /complgen/r... |
29d2c06cb76b5de69a4ca810ab9646ef685d881714ed586f3bff32d4b0b572a5 | Shell | 58,249 | 1,645 | #!/bin/bash
#: Title : test_fit_ppf
#: Date : 2023-06-30
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_ppf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
47ec40fe62c6e7209d39551b25aae5447b7cc6b1d3565b4f6676ca9ae2132703 | Shell | 60,152 | 983 | #!/bin/bash
#
# DWI POST processing using COMMIT with bash:
#
# POST processing workflow for tract-specific results.
#
# This workflow makes use of MRtrix3 and COMMIT framework (https://github.com/daducci/COMMIT)
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMEN... |
27e283233a5a4d2dad6cc95c16c36bccb978a92cde6a2b99fb049ab129bc4253 | Shell | 67,146 | 1,565 |
mkdir -p $rawLoc
mkdir -p $scratchLoc
mkdir -p $resultsLoc
mkdir -p $mtagscript
##############################################################################
# (II) Extract Conventional predictors:
#######################################
# create a backup for reproducibility, in case it gets updated
# cp /rds/proj... |
35396b0c1a431ed8d7edcb781af365aaa1fac204dcb674dd18bd7a4050f12306 | Shell | 67,153 | 1,565 |
mkdir -p $rawLoc
mkdir -p $scratchLoc
mkdir -p $resultsLoc
mkdir -p $mtagscript
##############################################################################
# (II) Extract Conventional predictors:
#######################################
# create a backup for reproducibility, in case it gets updated
# cp /rds/proj... |
15305c76f7522e1d4782c17a6fd0bfb43d5d1446a9a87d05cb1daba277faec74 | Shell | 71,052 | 1,184 | #!/bin/bash
# Taku Ito, 10/29/14. Modified by Ravi Mill for CPRO2_learning 03/16/18. Modified by Carrisa Cocuzza 2023 for Yale HPC and TCP dataset.
#########################
# IMPORTANT NOTES:
# 1. Assumes that dicom2nifti conversion has been carried out (e.g. as part of BIDS conversion). On Milgram, can module lo... |
f9d21f6e2262befe46400dc0ca7641dde4fcd74b5cd4e8764c81cbd8cc32d68a | Shell | 71,974 | 866 | #!/bin/bash
# This script builds a distributable directory contained version of R using the Holy build box environment
# options:
# -a|-arch|--arch: 64, x86_64 or linux-x86_64 for 64 bit Linux build (default); ix86, 32 or linux-ix86 for 32 bits Linux build; win, windows-x86_64 or mingw-w64 for Windows 64 bit build
# -... |
979bfb885bca2e119b338296e693b659224fb5810d355af9aae6a0478c231a5a | Shell | 78,481 | 1,288 | #!/bin/bash
# Taku Ito, 10/29/14. Modified by Ravi Mill for CPRO2_learning 03/16/18. Modified by Carrisa Cocuzza 2023 for Yale HPC and TCP dataset.
#########################
# IMPORTANT NOTES:
# 1. Assumes that dicom2nifti conversion has been carried out (e.g. as part of BIDS conversion). On Milgram, can module lo... |
78981fc4c80d7ec98603287c45bce1c664bc16f2ed6dedfc1f72271c7151dfa7 | Shell | 101,397 | 3,731 | #!/usr/bin/env bash
################################################################################
#
# This Bash script synchronizes multiple copies of the same file in the repository.
# Note that it is not robust against files that have whitespace in their names.
#
# Please keep this file organized in alphabetical o... |
6785aa8d879b1e0c21daacfa6bab3849e7e9eb1f95c31b4ed5d496f680ccbe22 | Stan | 319 | 19 | data {
int<lower=0> N;
int<lower=0> K;
int<lower=0> P;
vector[N] y[K];
matrix[N,P] x[K];
}
parameters {
vector[P] mu;
cov_matrix[P] Sigma;
real<lower=0> noiseVar;
}
model {
for (k in 1:K) {
y[k] ~ multi_normal( x[k] * mu, x[k] * Sigma * x[k]' + diag_matrix(rep_vector(noiseVar, N)));
}
}
|
06b956bc8da0d241636337f88a8d0c67e90b07e0992a457b170daabdb8aaf12f | Stan | 938 | 25 | data {
int<lower=0> N; // number of observations
real<lower=-pi(), upper=pi()> theta[N]; // observed theta
}
generated quantities {
real a; // slope
real<lower=-pi(), upper=pi()> b; // phase offset
real<lower=0> kappa; ... |
379f4a0246008dc98b24829437a853a8f683444d7dee10deec706286455aeaf7 | Stan | 1,398 | 48 | data {
int<lower=0> N; // number of observations
real<lower=-pi(), upper=pi()> theta[N];
real<lower=-pi(), upper=pi()> phi[N];
int<lower=0> N_grid; // number of grid points used for posterior predictives
real<lower=-pi(), upper=pi()> theta_grid[N_grid];
}
parameters {
real a; ... |
c95ed24b32552e9f6a7a51572c3fad2f065d60fe0c2cf012851f57154d7c1fbc | Stan | 1,598 | 70 | functions {
real Sigmodal(real x1, real x2, real delta, real alpha ) {
real S=(1.0/(1.0+exp(alpha*(x1-(delta*x2)))))-0.5;
return S;
}
}
data {
int ns;
int nt;
real dt;
int ds;
real alpha;
real g_1;
real g_2;
real g_3;
real g_4;
real delt... |
c5d934bf4f95815c4368c40aacc4d1554f93883e907f6b2405ff4414e4ea20a7 | Stan | 1,811 | 60 | // Stan model for pupil-baseline estimation
//
functions{
// asymmetric laplace function with the mu, sigma, tau parametrization
real my_skew_double_exponential_lpdf(real y, real mu, real sigma, real tau) {
return log(tau) + log1m(tau)
- log(sigma)
- 2 * ((y < mu) ? (1 - tau) * (mu - y) : ... |
268995694346f93428110381aa343ab53dee664b6db3d260b80509aacfae9af0 | Stan | 3,356 | 121 | functions {
real Sigmodal(real x1, real x2, real delta, real alpha ) {
real S=(1.0/(1.0+exp(alpha*(x1-(delta*x2)))))-0.5;
return S;
}
}
data {
int ns;
int nt;
real dt;
int ds;
real alpha;
row_vector[nt] xpy_obs;
int n_params;
row_vector[n_... |
5eb8a796f06609fab9efde17b2e0ef23edeb7d2db70b9b69faa12a5c2b28fceb | Stan | 3,356 | 121 | functions {
real Sigmodal(real x1, real x2, real delta, real alpha ) {
real S=(1.0/(1.0+exp(alpha*(x1-(delta*x2)))))-0.5;
return S;
}
}
data {
int ns;
int nt;
real dt;
int ds;
real alpha;
row_vector[nt] xpy_obs;
int n_params;
row_vector[n_... |
6c3d383f659ba05b88a1c9ddd6e03e61ebc0ba8b76ce2ed22b4b8470592187b5 | Stan | 3,356 | 123 | functions {
real Sigmodal(real x1, real x2, real delta, real alpha ) {
real S=(1.0/(1.0+exp(alpha*(x1-(delta*x2)))))-0.5;
return S;
}
}
data {
int ns;
int nt;
real dt;
int ds;
real alpha;
row_vector[nt] xpy_obs;
int n_params;
row_vector[n_... |
a27e1550ac0ea88767a9b39afc31594ee9e22fd7207bcf3e7effd4d7e0f5f310 | Stan | 3,356 | 121 | functions {
real Sigmodal(real x1, real x2, real delta, real alpha ) {
real S=(1.0/(1.0+exp(alpha*(x1-(delta*x2)))))-0.5;
return S;
}
}
data {
int ns;
int nt;
real dt;
int ds;
real alpha;
row_vector[nt] xpy_obs;
int n_params;
row_vector[n_... |
a66f96542760a768cc2c9e5cba9092fa93dab47c3acf79bc6bcee0642262f249 | Stan | 3,407 | 121 | functions {
real Sigmodal(real x1, real x2, real delta, real alpha ) {
real S=(1.0/(1.0+exp(alpha*(x1-(delta*x2)))))-0.5;
return S;
}
}
data {
int ns;
int nt;
real dt;
int ds;
real alpha;
row_vector[nt] xpy_obs;
int n_params;
row_vector[n_... |
65d849535b638d1f5b42fb5822278449da3a6625587bcc0951e511dd389b1741 | Stan | 3,426 | 122 | functions {
real Sigmodal(real x1, real x2, real delta, real alpha ) {
real S=(1.0/(1.0+exp(alpha*(x1-(delta*x2)))))-0.5;
return S;
}
}
data {
int ns;
int nt;
real dt;
int ds;
real alpha;
row_vector[nt] xpy_obs;
int n_params;
row_vector[n_... |
1956c2c09358b07676f40d67ff98fb87ad3a919f9e76a0e683e576647f231d79 | Text | 7 | 1 | # csgat |
be28463e05e58b9e20bc6622bdb53408fc364cd8289cf3beda8b8020f89e900b | Text | 13 | 1 | # Rpe_project |
3bfc2802ae715b685d9c04cafd6e8c4b1155a9fde7d2fa5897c12a04c1f61652 | Text | 26 | 1 | # Nageotte-Nodule-Analysis |
e15f4f5b3a7437451f4d77ba0e9b89cb8eaaad69145caa49987129f7e3fed652 | Text | 27 | 1 | Repository data for papers
|
47747edc485376878e6093f7f1ce447e19304a678b766fde2082ef81705bad5b | Text | 31 | 1 | # snRNA-seq-of-inulin_-Diet_FAD |
fd5209fcad3d70dfb1ef9ddbdf7bcade58bde788fde12594ad847e729941e502 | Text | 37 | 2 | # SPARK
SPARK toolbox for (di)graphs
|
7ed47403561337cffd788c1021f71aace517efcc816c03cbe324636b57b4e6e8 | Text | 47 | 1 | # Cabral-Calderin-Henry-Entrainment-Audio-tACS
|
5eefdd653f1ddfcde3e883c345c68e0dccab77d76d808815ee50fbea5aebed87 | Text | 58 | 1 | Analysis of cell counts for marmoset cingulotomy project
|
e6d7c15224eb7b8a0867847a7a33a58ba1cccf812c33a90198f7880ffdeaded9 | Text | 60 | 2 | # NEOBA
NEural Oscillation based Brain Age prediction model
|
9dc27175b87af71a0d57661ebdc6f81205c0f3aaac948b05e8a6ae88f342676c | Text | 71 | 2 | # CB_BMI_Analysis
CB-BMI analysis code: Gulati-lab (www.gulatilab.org)
|
376051899a83aabbe893702379b771b18ad1313cad5513c283c9581385eac50d | Text | 79 | 2 | # fib-sem-charge-mitigation
Data acquisition and processing scripts for FIBSEM
|
84925d6fdd78348c54b71299eed5014e41a76865ccec3f9c841e9129eff6dbb2 | Text | 79 | 2 | # HoleResponse
Repository for the Hole-Response experiment using line-scanning
|
a939f7985bcd97be33e06e73e37993cd248d059c6a23863741cae65c6ba87261 | Text | 85 | 3 | # HBMVNR
This repository will contain the HBM-VNR functions modeling the cerebelum.
|
cac48d39a5dd274080eda189370865f3428576e3558c227bf9c51ddd7fec1f96 | Text | 97 | 4 | trompy
======
Collection of tools for plotting and data analysis from McCutcheon Lab in Tromsø
|
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