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sotnir / NENAH-BIDS

A collaborate platform for streamlining a BIDS workflow for the NENAH study, on the linux workstation based at University of Southampton.
https://www.southampton.ac.uk/cndng
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Update segmentation.sh #147

Closed yukaizou2015 closed 2 years ago

yukaizou2015 commented 2 years ago

To add an option -hippocampal-subfields-T1 to run automated segmentation of hippocampus in subfields when called

Need to install Matlab Runtime (#17) to enable running this module.

yukaizou2015 commented 2 years ago

Some thoughts for implementations:

# https://unix.stackexchange.com/questions/432352/list-of-arguments-in-only-one-variable-in-bash

arg=()

if [ ! -f $subfields]
then
    args+=(-hippocampal-subfields-T1)
    echo recon-all $args
else
    echo recon-all
fi
yukaizou2015 commented 2 years ago

A different script segmentHA_T1.sh needs to be called, rather than expanding recon-all.

ERROR: the hippocampal subfield module is now in separate scripts:
#   segmentHA_T1.sh
# segmentHA_T1.sh SUBJECT_ID [SUBJECT_DIR]
# (the argument [SUBJECT_DIR] is only necessary if the
#  environment variable SUBJECTS_DIR has not been set
#  or if you want to override it)
# segmentHA_T1.sh sub-$sID $datadir