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Michael Krause
tardis-doc
Commits
efa02ee8
Commit
efa02ee8
authored
May 03, 2021
by
Michael Krause
🎉
Browse files
Fix bash syntax highlighting
parent
3dcc9863
Changes
1
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software/fsl.rst
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efa02ee8
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@@ -36,16 +36,16 @@ for all combinations of subjects and runs in parallel all in one go:
.. code-block:: bash
for subject in ID1 ID2 ID3; do
for subject in ID1 ID2 ID3; do
for run in 1 2 3 ; do
# create a copy of the template with a unique name
featfile="design.${subject}.${run}.fsf"
cp design.template $featfile
# replace the placeholder by actual values
sed -i "s|%SUBJECT%|$subject|g" $featfile
sed -i "s|%RUN%|$run|g" $featfile
# submit the feat command with the current design file
sbatch --wrap ". /etc/profile ; module load fsl ; feat $featfile"
done
...
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@@ -62,7 +62,7 @@ parallelize over a number of subjects. Example:
.. code-block:: bash
for icadir in *ica ; do
echo
'
#!/bin/bash" > tmp.sh
echo
"
#!/bin/bash" > tmp.sh
echo "module load fsl_fix" >> tmp.sh
echo "source /etc/fsl/5.0/fsl.sh" >> tmp.sh
echo "fix ${icadir} /opt/software/fix/1.06/training_files/Standard.RData 20" >> tmp.sh
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