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This script will run the FreeSurfer stats.

Usage: fsRunStats.sh dataFile nameOfAverageSubject outputPrefix [options]

Performs the following:
1. Parse the input file, checking directories exist, and checking which patient is in which group.
2. For each group, we extract thickness, volume, mean curvature and area for each hemisphere,
and then volume and mean for the whole brain.
3. Generates an average subject, using all your groups.
4. Resamples each surface to your average average subject.
5. Extracts cortical thickness at each vertex for each patient, storing in a .mgh file.

Mandatory Arguments:

dataFile : is a file containing your patient names and groups.

e.g.
patient group
BROLI 0
CHARO 0
CLAPA 1
FARSA 1

The CONTROL group should be group zero.
Group numbers must be successive positive integers.
If you specify a negative number, that patient will be ignored.

nameOfAverageSubject : The name of the average subject to output.

outputPrefix : A simple text identifier to group together all your results.
eg. "baseline" or "00" or "matt".

Options:

-fwhm : fwhm [ default 20 ]
-start : Step to start at [ default 1 ]
-stop : Step to stop at [ default 5 ]
-nv : No average volume [ default is to do the volume ]
-email : Your email address.

-inputPrefix : Used if you want to re-run step 5,
with different FWHM. You can specify
the prefix of the non-blurred file.