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It usual to have many FreeSurfer recon-all commands to process multiple datasets.

This procedure helps to automate this:
If you need to run recon-all many times (eg, you have many subjects),
then you can run the following commands (in cshell) to launch many
commands. Below, the script cd's into the $SUBJECTS_DIR where it is
assumed th that the only files or folder that are there are your
subjects' folders. In this case, they must have already been
set up with the raw data in $SUBJECTS_DIR/$subject/mri/orig/
If you have many processors and enough memory, you can
process many simultaneously by adding an ampersand (&) after
recon-all -subjid $i -all (eg, "recon-all -subjid $i -all&")
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SETENV SUBJECTS_DIR $PWD setenv SUBJECTS_DIR $PWD

If you need to run recon-all many times (eg, you have many subjects), then you can run the following commands (in cshell) to launch many commands. Below, the script cd's into the $SUBJECTS_DIR where it is assumed th that the only files or folder that are there are your subjects' folders. In this case, they must have already been set up with the raw data in $SUBJECTS_DIR/$subject/mri/orig/ If you have many processors and enough memory, you can process many simultaneously by adding an ampersand (&) after recon-all -subjid $i -all (eg, "recon-all -subjid $i -all&")

cd your_study_group_data
setenv SUBJECTS_DIR $PWD
foreach i (*)
echo $i
recon-all -subjid $i -all
end

Wait some days...

UserContributions/Scripts/Two (last edited 2016-10-18 16:48:21 by 172)