diff --git a/fsl_glm_magdeburg_style.sh b/fsl_glm_magdeburg_style.sh index d96e428..33d8311 100755 --- a/fsl_glm_magdeburg_style.sh +++ b/fsl_glm_magdeburg_style.sh @@ -5,6 +5,7 @@ # set -e -u +set -x # remember the original directory, just to make some admin parts easier # but generally irrelevant @@ -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 ---