Alexander Li Cohen alexlicohen
alexlicohen
/ cbig_2BP_parallel.sh
Last active
August 26, 2021 21:23
[CBIG script for 2BP servers] #bchcohenlab #shell #CBIG #parallel
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| export study=ABIDE1 | |
| export site=SBL | |
| /fileserver/caladan_ssd/repos/BIDS_to_CBIG_fMRI_Preproc2016/BIDS_parallel_list_one_server.sh \ | |
| 60 \ | |
| /fileserver/caladan_ssd/repos/BIDS_to_CBIG_fMRI_Preproc2016/BIDS_2BP_CBIG_fMRI_preprocess_sesAware_phase.sh \ | |
| /fileserver/gammu/collections/${study}/${site} \ | |
| /fileserver/gammu/projects/${study}/subject_lists/${site}_subject_list.txt \ | |
| /fileserver/gammu/projects/${study}/freesurfer_v7.1.0/${site} \ | |
| /fileserver/gammu/projects/${study}/CBIG_fMRI_preprocess_ABIDE/${site} \ |
alexlicohen
/ movedocker.sh
Last active
June 23, 2021 16:16
[moving docker home] moving the default docker image location out of the root partition #cohenlab #docker #shell
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| # as root: | |
| systemctl stop docker | |
| cd /home_local/ | |
| mkdir docker | |
| chmod a+w docker/ | |
| rsync -avxP /var/lib/docker/ /home_local/docker | |
| nano /lib/systemd/system/docker.service | |
| # change: |
alexlicohen
/ git_clone_branch.sh
Created
June 23, 2021 13:14
[github shallow branch clone] #cohenlab #github #git
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| # This creates a shallow clone (good for docker) of a specific branch. | |
| git clone --depth 1 --branch compiled-for-MCR https://github.com/bchcohenlab/CBIG.git CBIG_compiled-for-MCR |
alexlicohen
/ bonding.sh
Last active
June 23, 2021 13:14
[network bonding notes] #cohenlab #shell #networking
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| # Show existing connections (/etc/sysconfig/network-scripts) | |
| nmcli -p dev status | |
| # Make new bonding connection | |
| nmcli con add type bond con-name bond0 ifname bond0 mode 6 | |
| # Bond existing ports to bond0 | |
| nmcli con add type bond-slave ifname p2p1 master bond0 | |
| nmcli con add type bond-slave ifname p2p2 master bond0 |
alexlicohen
/ raid_id.sh
Last active
June 23, 2021 13:15
[raid setup on ecaz] step to ID and setup new RAID array #cohenlab #unix #centos
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| # setup raid in iDRAC | |
| # in OS, switch to root and get a list of attached devices | |
| su - | |
| lsblk | |
| # partition | |
| parted -a optimal /dev/sda | |
| #(in parted): |
alexlicohen
/ gsp_prep.sh
Last active
April 17, 2021 10:33
[GSP Prep for Dataverse] Steps I did to prep the CBIG output for Dataverse #cohenlab #GSP #shell
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| mkdir -p derivatives/CBIG_fMRI_Prepoc2016_modified | |
| mv sub* derivatives/CBIG_fMRI_Prepoc2016_modified/ | |
| cd derivatives/CBIG_fMRI_Prepoc2016_modified | |
| for i in `ls */*/*gz`; do fslreorient2std $i; done | |
| for i in `ls`; do | |
| mkdir ${i}/anat | |
| mkdir ${i}/func | |
| mv ${i}/vol/norm_MNI152_1mm.nii.gz ${i}/anat/${i}_norm_MNI152_1mm.nii.gz |
alexlicohen
/ using_retrieve2.sh
Created
February 9, 2021 15:48
[BCH PACS script] Retriving data from the clinical PACS #cohenlab #PACS
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| /home/ch163210/bin/retrieve2.sh [MRN] [STUDY DATE] [OUTPUT DIRECTORY] [MODALITY] |
alexlicohen
/ dcm2niix_loop.sh
Last active
February 10, 2021 15:32
[dcm2niix loop] script to process DICOMs with dcm2nixx and ID sequences #cohenlab #shell #dcm2niix
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| for i in `ls -d 1*/`; do dcm2niix -b y -ba y -z o -f '%i_%n_%3s_%d_%p' -o /Volumes/Drobo/Research/Dhand_2nd_set/dhand_bids /Volumes/Drobo/Research/Dhand_2nd_set/${i}; done |
alexlicohen
/ double_rsync.sh
Last active
June 22, 2021 00:17
[BCH to BWH transfer] how to double rsync data across firewalls #cohenlab #rsync #E2 #ERISOne
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| rsync -e ssh -ahvzP /lab-share/Neuro-Cohen-e2/Public/projects/GSP/GSP1000_MF alex@172.18.206.42:/Volumes/Drobo/Research/collections/ | |
| rsync -ahzP /lab-share/Neuro-Cohen-e2/Public/connectomes/GSP1000_500M alex@172.18.219.214:/Volumes/Drobo/Research/connectomes/ | |
| rsync -avhzP /Volumes/Drobo/Research/collections/GSP1000_MF ayc57@erisonexf.partners.org:/data/nimlab/Data_from_Alex_BCH/ | |
| rsync -avhzP /Volumes/Drobo/Research/connectomes/GSP1000_* ayc57@erisonexf.partners.org:/data/nimlab/Data_from_Alex_BCH/ | |
| # getting the surface files: | |
| # on E2, in projects/GSP/CBIG_fMRI_preprocess_Legacy_GSP_surfaceBased_standard: |
alexlicohen
/ simple_rclone.sh
Created
January 12, 2021 15:09
[rclone GDrive to E2] #cohenlab #rclone #gdrive #E2
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| rclone sync drive_cohenlab_Inbox: /lab-share/Neuro-Cohen-e2/Public/lesions/WKTang_bids/sourcedata/secondbatch --progress |
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