Hi Catherine,
I use a very simple linux bash script for each DTI pre-processing stage. For eddy_correct, for example, you'd want something like this:
#!/bin/bash
#Put me in your /home/bin, and remember to make me executable with something like chmod a+rwx "title of linux script here".
subjs="list your subjects here e.g. con1 con2 pat1 pat2"
#Put your main directory here (contains a folder for con1, con2, etc)
cd /imaging/username/DTIanalysis/
#Assuming that you have a folder for each subject in /DTIanalysis/ and that in each subject's folder, you have a 4D .nii datafile containing the diffusion volumes, called data.nii.gz
for s in ${subjs} ; do
echo "Eddy correcting data for subject ${s}"
eddy_correct ${s}/data.nii.gz ${s}/data_ec.nii.gz 0
done
Edit the commands between "for" and "done" in the for loop according to what preprocessing stage you want to run.
Hope that helps,
Charlotte
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Charlotte Rae
MRC Cognition and Brain Sciences Unit
Cambridge, UK
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