-------------------------------------------
 The File -> New Subject menu creates a new
 blank subject and its standard subdirectories
-------------------------------------------
This is the first step when making a new
*manually-reconstructed* (e.g., hi-res) subject.

Note that this step is *not* necessary for a
subject made with the standard MGH pipepline
using MGHTools -> Run Recon-all.  For help
with that, see Help -> Run Recon-all.

The subject directory (either made here or by
recon-all) must exist *before* a new csurf
functional session can be made for this subject.

The default location in which to create the new
empty subject directory is the current setting of
the environment variable, SUBJECTS_DIR, but a
subject directory can be made anywhere.  If the
parent directory of the new subject is not the
current SUBJECTS_DIR, SUBJECTS_DIR will be
changed to the new parent for this copy
of csurf.

To permanently change the startup SUBJECTS_DIR,
edit its definition in your shell startup file
(for csh/tcsh edit .cshrc/.tcshrc, or for
sh/bash, edit .bashrc/.bash_profile).

Finding subjects is easiest with csurf if they
are stored together in the same SUBJECTS_DIR.
Multiple functional sessions for a single subject
can access a single SUBJECTS_DIR subject's
surfaces, labels, etc.

The standard subject directory structure is:

SUBJECTS_DIR		root of a subjects database
   subjname/		e.g., first3/last3 initials
      scripts/		NOTES, configs, special scripts
      mri/		3D MRI data
         orig.mgz		original scan
         orig/		[CORdir equiv, incl's 001.mgz]
         T1.mgz		brightness-norm'd T1
         T1/		[CORdir equiv]
         PD.mgz		for strip skull (optional)
         PD/		[CORdir equiv]
         PDbrain.mgz		skull-stripped PD
         PDbrain/		[CORdir equiv]
         brain.mgz		skull-stripped T1
         brain/		[CORdir equiv]
         wm.mgz		filtered white matter
         wm/		[CORdir equiv]
         filled.mgz		rh,lh filled white matter
         filled/		[CORdir equiv]
         tmp/		tmp images
         transforms/		Talairach, etc
      surf/		surface/curv/area/etc files
      bem/		stripskull ico, EEG/MEG ico
      label/		subject-specific labels
      rgb/		saved subject bitmaps
      mpg/		saved subject movies
      tmp/		send/goto point, etc

There are four additional directories created by
recon-all:

      src/		src
      stats/		stats
      touch/		cmdlines
      trash/		trash

Manual Hi-Res Reconstruction

Once the subject has been made, T1-weighted raw
scan(s) (e.g., 1mm^3 or higher res) should be
copied into separate subdirectories of the
mri/orig directory of that subject.  The
subdirectories you make in there can have any
name.  For example:

  $SUBJECTS_DIR/somesubject/mri/orig/mprage1/*
  $SUBJECTS_DIR/somesubject/mri/orig/mprage2/*

The Setup Struct Scans menu looks in the mri/orig
directory to find subdirectories, each of which
should contain a single scan, and averages them.

MGHTools -> Run Recon-all

Setup Struct Scans is *not* necessary to average
scans with MGHTools -> Recon-all.  See HOWTO
instructions for averaging scans on the Run
Recon-all panel when it is opened.

