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Finish magdeburg-style script #1

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May 23, 2018
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25 changes: 21 additions & 4 deletions fsl_glm_magdeburg_style.sh
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
#

set -e -u
set -x

# remember the original directory, just to make some admin parts easier
# but generally irrelevant
Expand All @@ -29,15 +30,31 @@ datalad remove --nocheck demo_func
# XXX actual demo from here

# -- part 0: RAWRAW data ---
# assemble all data artifacts as the were produced in a dataset that
# assemble all data artifacts as they were produced in a dataset that
# represents the state of data acquisition that cannot be reproduced
# without from scratch re-acquisition

TODO
datalad cbbs-create-study study_ds
cd study_ds
datalad cbbs-import-dcm ${wdir}/s02_study_dicoms.tar.gz
cp ${wdir}/s02_log.tsv 02/
datalad add 02/ -m "Add stimulation log"
cd ${wdir}

# -- part 1: DICOM conversion ---
datalad create bids
cd bids

# get a ready-made container with the dicom converter
datalad containers-add conversion -u shub://mih/ohbm2018-training:heudiconv

TODO
# install input data as a subdataset, to enable identity tracking
# an automated content retrieval, if necessary
datalad install -d. -s ../study_ds sourcedata
mkdir -p inputs; ln -s ../sourcedata inputs/rawdata; datalad add inputs/rawdata

# Run the conversion TODO: description (see amazing_datalad)
datalad cbbs-spec2bids -s sourcedata/02
cd ${wdir}

# -- part 2: (GLM) analysis ---

Expand Down