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
foreach i (*)
echo $i
recon-all -subjid $i -all

Wait some days...

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