Alexander Li Cohen alexlicohen
alexlicohen
/ E2_CBIG_Legacy.sh
Created
June 20, 2020 01:55
[E2 slurm CBIG Legacy command] Running the CBIG Legacy script on a BIDS directory with slurm #cohenlab #slurm #BIDS #E2 #CBIG
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| /lab-share/Neuro-Cohen-e2/Public/repos/e2scripts/sbatch_script_bids_target_sublist.sh \ | |
| /lab-share/Neuro-Cohen-e2/Public/repos/e2scripts/single_CBIG_Legacy.sh \ | |
| /lab-share/Neuro-Cohen-e2/Public/collections/GSP \ | |
| /lab-share/Neuro-Cohen-e2/Public/projects/GSP \ | |
| /lab-share/Neuro-Cohen-e2/Public/projects/GSP/GSP1000.txt |
alexlicohen
/ clone_to_fork.sh
Created
June 19, 2020 11:31
[git clone to git fork] Converting from a clone of a public repo to your own fork to generate a PR without re-cloning #cohenlab #github #CBIG
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| # On github, fork the public repo: here, I went from https://github.com/ThomasYeoLab/CBIG to https://github.com/bchcohenlab/CBIG.git | |
| git remote rename origin upstream | |
| git remote add origin https://github.com/bchcohenlab/CBIG.git | |
| git fetch origin | |
| git branch --set-upstream-to origin/master master | |
| git pull |
alexlicohen
/ CBIG_E2_test.sh
Last active
June 20, 2020 01:56
[E2 CBIG test command] Running the CBIG preproc pipeline on one BIDS subject on E2 #cohenlab #BIDS #E2 #CBIG #GSP
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| /lab-share/Neuro-Cohen-e2/Public/repos/BIDS_to_CBIG_fMRI_Preproc2016/BIDS_E2_CBIG_fMRI_preprocess.sh \ | |
| /lab-share/Neuro-Cohen-e2/Public/collections/GSP \ | |
| /lab-share/Neuro-Cohen-e2/Public/projects/GSP/freesurfer_v4.5.0 \ | |
| /lab-share/Neuro-Cohen-e2/Public/projects/GSP \ | |
| sub-0001 \ | |
| /lab-share/Neuro-Cohen-e2/Public/repos/BIDS_to_CBIG_fMRI_Preproc2016/configs/Legacy.config |
alexlicohen
/ BIDS_parallel_usage.sh
Last active
June 20, 2020 01:56
[Corrin CBIG with parallel] Usage for Alex's BIDS_parallel.sh #cohenlab #shell #BIDS #CBIG #parallel
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| #!/bin/bash | |
| # Scripts are here: https://github.com/bchcohenlab/BIDS_to_CBIG_fMRI_Preproc2016 | |
| # Usage for Whole BIDS directory: | |
| # BIDS_parallel.sh <number_of_threads> <script_to_run> <bids_dir> <all_the_arguments> | |
| # BIDS_parallel_list.sh <number_of_threads> <script_to_run> <bids_dir> <list> <all_the_arguments> | |
| #Examples: | |
| /fileserver/caladan_ssd/repos/BIDS_to_CBIG_fMRI_Preproc2016/BIDS_parallel.sh 60 \ | |
| /fileserver/caladan_ssd/repos/BIDS_to_CBIG_fMRI_Preproc2016/BIDS_CBIG_fMRI_preprocess.sh \ |
alexlicohen
/ rsync_parallel.sh
Last active
May 26, 2021 20:17
[parallel bids rsync example] Here's how I copied the ABCD1000 from e2 to corrin #cohenlab #bids #E2 #bash #rsync
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| #!/bin/bash | |
| for i in `cat ABCD1000.txt`; do | |
| echo rsync -ravhP --delete -e ssh \ | |
| /reference_databases/RestrictedAccessDatabase/Dropoff_Alex/abcdbids/s3/sub-${i}/ \ | |
| ch186161@corrin:/local_raid/collections/ABCD/sub-${i}/ >> commands.txt | |
| done | |
| parallel --eta --jobs 4 < commands.txt |
alexlicohen
/ slurm_FSv4.5.sh
Last active
June 20, 2020 01:55
[E2 slurm FSv4.5 singularity script with sublist] Command to run a singularity-based pipeline on E2 from a subject list (avoids vServers) #cohenlab #E2 #singularity #BIDS #slurm
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| #!/bin/bash | |
| /lab-share/Neuro-Cohen-e2/Public/repos/e2scripts/sbatch_script_bids_target_sublist_exclude.sh \ | |
| /lab-share/Neuro-Cohen-e2/Public/repos/e2scripts/single_freesurfer_v4.5.sh \ | |
| /lab-share/Neuro-Cohen-e2/Public/collections/GSP \ | |
| /lab-share/Neuro-Cohen-e2/Public/projects/GSP/freesurfer_v4.5.0 \ | |
| /lab-share/Neuro-Cohen-e2/Public/projects/GSP/GSP1000.txt |
alexlicohen
/ BIDS_to_datalad.sh
Last active
February 14, 2023 07:59
[Adding Datalad to BIDS dir] Shell commands to add Datalad subdatasets #cohenlab #shell #datalad #BIDS
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| #!/bin/bash | |
| # in study dir: | |
| # Create superdataset | |
| datalad create -c text2git --force | |
| for i in `ls -d sub-*`; do | |
| if [ ! -d "${i}/.git" ]; then | |
| # Create and register the subdataset | |
| datalad create -c text2git --force -d . $i |
alexlicohen
/ BIDS_manufacturer_grep.sh
Last active
June 16, 2020 20:18
[BIDS Scanner Ident] Quick grep to find the scanner manufacturer for a large multi-site dataset #cohenlab #BIDS #shell #abcd
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| #!/bin/bash | |
| for i in `ls -d sub-*/`; \ | |
| do echo $i `grep '"'Manufacturer'"' ${i}/ses-baselineYear1Arm1/func/sub*_ses-baselineYear1Arm1_task-rest_run-01_bold.json` >> scanner_list; done |
alexlicohen
/ Singularityfile
Last active
June 10, 2020 11:04
[Freesurfer v4.5.0 Singularity Recipe] Recipe for Building a Centos 6 container with FS v4.5 (req license.txt in same dir) #cohenlab #singularity #freesurfer
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| Bootstrap:docker | |
| From:centos:6 | |
| %files | |
| license.txt /opt/freesurfer/.license | |
| %environment | |
| FREESURFER_HOME=/opt/freesurfer | |
| SUBJECTS_DIR=/output |
alexlicohen
/ download.sh
Last active
June 16, 2020 20:18
[D/L the ABCD to E2] Command used to download the ABCD-BIDS release from Damien's DCAN using their tool #cohenlab #shell #E2 #abcd
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| #!/bin/bash | |
| #After logging into E2 | |
| srun -A bch -p bch-interactive -n 16 --mem=16GB --pty /bin/bash | |
| python3 /lab-share/Neuro-Cohen-e2/Public/repos/nda-abcd-s3-downloader/download.py \ | |
| -i datastructure_manifest.txt \ | |
| -o /reference_databases/RestrictedAccessDatabase/Dropoff_Alex/abcdbids/s3 \ | |
| -d data_subsets_inputs_only.txt \ | |
| -p 16 |