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

[Eugene Zeien]

The problem is, BRAINS cannot identify the _ACPC directory.
So, the procedure "getACPCdir" returns -1.  Thus, the
message you noted,
     b2 save mask -1/grey_plugs.mask brains2 m29
BRAINS is trying to save the grey_plugs.mask in a directory
called "-1", which probably doesn't exist :-)

Frequently, this is caused by starting BRAINS in some directory
other than the 10_ACPC ( I assume, since the image is Patient-ID_10_T1.img,
you resampled to 10_ACPC)

Given the mask number, m29, I'll bet you've gone through most of
the preparation steps without exiting brains2.  Try starting brains2
in the 10_ACPC directory and then go through the segmention procedure.

Hans Johnson wrote:
> ------ Forwarded Message
> 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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> 
> ------ End of Forwarded Message
> 
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