1-dataSetup_BIDS

#!/bin/bash

# License
# This file is part of the project megFingerprinting. All of megFingerprinting code 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 option) any later version.
# megFingerprinting is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
# more details. You should have received a copy of the GNU General Public License along with megFingerprinting.
# If not, see <https://www.gnu.org/licenses/>.

# Background
# This script needs to be run from the local computer!
# Give the shell permission to execute this: chmod 755 1-dataSetup_BIDS
# Type ./1-dataSetup_BIDS to run it

# Constants
BIC_PATH="jdscasta@login.bic.mni.mcgill.ca:/meg/meg2/omega/OMEGA_BIDS"
LOCAL_PATH="/media/jdscasta/Jason_drive/omega_data/data/OMEGA_BIDS_2"
BIC_PREPROC_ANAT="jdscasta@login.bic.mni.mcgill.ca:/meg/meg2/omega/OMEGA_BSTdb/OMEGA_BSTdb_v1/anat"

# Create subject txt file
ssh jdscasta@login.bic.mni.mcgill.ca ls -d /meg/meg2/omega/OMEGA_BIDS/sub-0* > $LOCAL_PATH/subs.txt

# Download the extra docs from the BIC server
scp $BIC_PATH/CHANGES.txt $BIC_PATH/dataset_description.json $BIC_PATH/NisoEtAl2015_OMEGA.pdf $BIC_PATH/OMEGA_README.pdf $BIC_PATH/participants.tsv $LOCAL_PATH

# From the full subs.txt, take n people
sed -n -e 1,220p $LOCAL_PATH/subs.txt > $LOCAL_PATH/subset_subs.txt

# Download n amount of subjects (session 1 or 2; change below to either ses-0001 to ses-0002, anatomy is in ses-0001), but only if they have anatomy data
for sub in $( cat $LOCAL_PATH/subset_subs.txt )
do
    if ssh jdscasta@login.bic.mni.mcgill.ca [ -d ${sub}/ses-0001/anat ]; then
        mkdir $LOCAL_PATH/${sub:(-8)}
        mkdir $LOCAL_PATH/${sub:(-8)}/ses-0002
        rsync -av $BIC_PATH/${sub:(-8)}/*.json $LOCAL_PATH/${sub:(-8)}/ses-0002
        rsync -av $BIC_PATH/${sub:(-8)}/ses-0002/meg $LOCAL_PATH/${sub:(-8)}/ses-0002
        rsync -av $BIC_PREPROC_ANAT/${sub:(-8)}/ $LOCAL_PATH/${sub:(-8)}/ses-0002/anat
    else
        echo "${sub:(-8)} has no anatomy files!" >> $LOCAL_PATH/subs_noAnat.txt
    fi
done

# Download metadata and empty room recordings
rsync -av $BIC_PATH/subject_metadata $LOCAL_PATH
rsync -av $BIC_PATH/sub-emptyroom $LOCAL_PATH