@@ -172,14 +172,14 @@ datalad run -m "Downgrade/Freeze mriqc container version" \
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# hardcode for mriqc to workaround an issue. So let' s remove it
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datalad run -m " Remove ad-hoc option for mriqc for older frozen version" sed -i -e ' s, --no-datalad-get,,g' .datalad/config
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# Install input data:
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- datalad install -d . -s https://github.com/ReproNim/ds000003-demo sourcedata
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+ datalad install -d . -s https://github.com/ReproNim/ds000003-demo sourcedata/raw
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# Setup git to ignore workdir to be used by pipelines
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echo " workdir/" > .gitignore && datalad save -m " Ignore workdir" .gitignore
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# Execute desired preprocessing while creating a provenance record
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# in git history
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datalad containers-run \
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-n bids-mriqc \
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- --input sourcedata \
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+ --input sourcedata/raw \
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--output . \
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' {inputs}' ' {outputs}' participant group -w workdir
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)
@@ -220,7 +220,8 @@ Now let's take a look at what we have.
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```
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/ds000003-qc # The root dataset contains everything
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- |--/sourcedata # we call it source, but it is actually ds000003-demo
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+ |--/sourcedata
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+ | raw/ # we call it source, but it is actually ds000003-demo "raw" BIDS dataset
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|--/code/containers # repronim/containers, this is where our non-custom code lives
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```
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@@ -289,7 +290,7 @@ Now we use `datalad containers-run` to perform the analysis.
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```bash
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datalad containers-run \
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-n bids-mriqc \
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- --input sourcedata \
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+ --input sourcedata/raw \
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--output . \
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' {inputs}' ' {outputs}' participant group -w workdir
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```
@@ -316,7 +317,7 @@ Date: Wed Jun 5 15:41:59 2024 -0400
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"code/containers/images/bids/bids-mriqc--0.16.0.sing"
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],
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"inputs": [
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- "sourcedata"
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+ "sourcedata/raw "
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],
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"outputs": [
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"."
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