[Brains-users] Some questions regarding segmentation

[Ronald Pierson]

Hi - sounds like you are making good progress!

This is a single file where the data from all of the scans that you
process will end up.  It is not necessary to update the global data
file, as the data for each scan is there in the 10_ACPC/standard
directory.  However, for us this makes it easy to put all the data in
one spot.  At Iowa we have about 10 different people doing standard
workup for the various researchers, and there are several thousand
scans.  For the data manager, this makes it simple because nobody has to
let him know when a scan is done, the data just ends up in the global
data file.  In one file he can see the new data from all of the scans
that have been completed.

This file name and path for this global data file can be changed when
you measure the volumes, or it can be changed permanently in a file
called brains2rc.  There is one of these files located somewhere in the
brains2 program folders, I don't recall where at the moment and I'll
email that later today when I am in the office.  You should copy that
file over to your linux home directory and modify it for your own
preferences.  Save it as .brains2rc (that makes it a hidden file).  The
settings you make in the brains2rc file in your home directory will
override those of the global one, so you can have your own personal
settings.  Somewhere near the bottom the brains2rc file the global data
file is set, just change it to whatever you want for your system.

FYI - the T50 volumes will probably not be useful to you, as they are
simply CSF vs. Tissue on the T1 image.  Segmentation volumes use the
tissue classified image, and divide the measures into gray, white, csf,
blood, and unclassified.

Ronald


-----Original Message-----
From: brains-users-bounces at psychiatry.uiowa.edu
[mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of
christma at zi-mannheim.de
Sent: Thursday, January 26, 2006 3:09 AM
To: brains-users at psychiatry.uiowa.edu
Subject: Re: [Brains-users] Some questions regarding segmentation

hi,

using the workup - measure T50 volumes I get all 
informations about the different volumes of different parts 
of the brain in a window (chek T50 volumes). All volumes are 
in the normal range accorcing to the displayed means and 
standard deviations. However, while trying to UPDATE I get 
the following error message

Failed to open global raw volume data file
/raid0/data/new_data/brains2/t50/t50_volumes_raw.dat

Usually I do create the missing directories manually - whta 
usually makes this kind of errors disappear. But I am not 
quite sure if I should create the directory on the root 
level.

Thanks for any hints in advance

Christoph

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