[Brains-users] FW: problems with Brains 2...

[Hans Johnson]

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From: konstantinos kokkalas <kokkalas_kostas at yahoo.com>
Date: Thu, 20 Oct 2005 10:03:44 -0700 (PDT)
To: <hans-johnson at uiowa.edu>
Subject: problems with Brains 2...

Dear Mr. Johnson


My name is Kokkalas Konstantinos and I am medicine
student at the University of Frankfurt /Germany.I
participate in a study about Alzheimer¹s disease
(under the supervision of  Prof. Dr. med Johannes
Pantel).The progress of the study requires the
successful  use of  the Brains 2 program. Our
colleagues in the University of Heidelberg, have
introduced me to the principals of this program.
Unfortunately I am facing some problems which do not
allow me to use it properly, although I followed all
the instructions of the installation that I got from
Heidelberg. I  have also got help from two scientists
who work in our University and are familiar with Linux
and other software.  I have reached a point where they
can not help me anymore, so they suggested to send you
this mail.
I am using this program on a desktop pc which meets by
far the hardware requirements, under the latest Linux
SUSE version. At the beginning I tried to work with an
older version of Brains 2 (Februar 2004 version).I
have had some crashes but the main problem was , that
by the segmentation of the brain I have had extremely
wrong kappa-values, which resulted in unusable results
by the measurement of the segmentation volumes. Now we
have installed in another computer the newest version
of Brains 2 (version of 27 July 2005) under the same
Linux platform. It seems to work better (no more
crashes), but as I try to segment the brain I get the
following message:   Failed to save gray mask
-1/grey_plugs.mask 
At the console report the   following message can be
seen:     Writing output plug masks.
b2 save mask -1/grey_plugs.mask brains2 m29
SIMPLE_ERROR: Filter failed to write the mask file
properly Module: 
/scratch/hjohnson/src/brains2/src/iplKernel/bkrwMask.cxx
Function: 
bk_writeMask Line: 595 Code: 12345678

The way by which I try to segment the brain is the
following:
WORKUP-  RUN SEGMENT-  BRAINS 2- click on IMAGE (top
250 voxels appears)- I load the Patient-ID_10_T1.img
and brain.mask which I have both created before- NEXT-
 NEXT-  FINISH- click off BOOTSTRAP-  RUN.

At the end of this procedure I get the message that I
mentioned before. The segment of the brain seems to be
working correctly; it seems to me that the program
cannot save the results.
I also have to mention ,that in order to exclude the
possibility the images we use to be the source of this
problem we have tested in Heidelberg a view of them
and they are working properly.
I am looking forward to your response.
Thank you very much in advance

With regards 
Konstantinos Kokkalas



  
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