[Brains-users] Some questions regarding segmentation

[Ronald Pierson]

The permissions/group errors are due to the way we use groups locally, and I
think that it is documented somewhere on the WIKI page.  We use a stdwrkup
group to make sure only those who are supposed to do standard workup have
the ability to modify key files.  You may either need to add that group, or
possibly modify the brains2 configuration so that this group isn't needed by
brains2.  Anyone have a better answer for that?

The problem of no csf is one I just noticed yesterday on a scan I was
running, and I hadn't submitted a bug report yet because I needed to verify
I hadn't introduced a problem in the workup myself.  Since you get the same
problem as I got, I am beginning to think it probably is a bug, and will
need to submit it.  I think everyone should check into how to report bugs
and also to see what bugs are reported.  This is on the web site.

I'll keep you posted on the histogram/T50 CSF bug or problem, as I don't
know what the problem is quite yet.

Ron



-----Original Message-----
From: brains-users-bounces at psychiatry.uiowa.edu
[mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of Christoph
Christmann
Sent: Thursday, January 26, 2006 9:50 AM
To: brains-users at psychiatry.uiowa.edu
Subject: RE: [Brains-users] Some questions regarding segmentation

Dear Eugene, dear Ronald,

I am did good progress in correcting the brain mask.
However, using the T50 algorithm I ended up with two error
messages

Error: Failed to change group and permission on old
measurement file /home/.../Pat6_10_ACPC/standard/
Standard_Volumes.old

and

Error: Failed to change group and permission on standard
measurement file /home/.../Pat6_10_ACPC/standard/
Standard_Volumes

Between both messages I get the message

"failed to generate histogram threshold module" in the
terminal window. I end up with the following data - there is
obviously no CSF measured.


Thanks again for any hint!

Christoph


  Left Brain Tissue    568.790    621.980     67.980
                 Left Brain CSF      0.000     82.140     27.
600
             Right Brain Tissue    569.151    634.270     70.
720
                Right Brain CSF      0.000     78.290     26.
800
        Left Cranial Box Tissue    568.705    621.820     68.
000
           Left Cranial Box CSF      0.000     81.970     27.
550
       Right Cranial Box Tissue    569.112    634.100     70.
750
          Right Cranial Box CSF      0.000     78.100     26.
740
       Left nFrontal Box Tissue    187.224    198.020     26.
370
          Left nFrontal Box CSF      0.000     30.970     12.
530
      Right nFrontal Box Tissue    181.408    210.220     28.
870
         Right nFrontal Box CSF      0.000     29.580     12.
590
       Left Temporal Box Tissue     99.858    112.370     12.
750
          Left Temporal Box CSF      0.000     14.970      5.
430
      Right Temporal Box Tissue    100.437    113.750     13.
140
         Right Temporal Box CSF      0.000     12.070      4.
710
       Left Parietal Box Tissue    106.293    119.200     14.
680
          Left Parietal Box CSF      0.000     14.650      6.
320
      Right Parietal Box Tissue    109.642    121.620     15.
300
         Right Parietal Box CSF      0.000     14.210      6.
170
      Left Occipital Box Tissue     49.095     62.580     10.
420
         Left Occipital Box CSF      0.000      5.190      3.
020
     Right Occipital Box Tissue     53.678     58.210      9.
910
        Right Occipital Box CSF      0.000      5.340      3.
000
     Left Cerebellum Box Tissue     61.491     67.440      9.
420
        Left Cerebellum Box CSF      0.000      7.620      2.
990
    Right Cerebellum Box Tissue     62.638     66.040      9.
170
       Right Cerebellum Box CSF      0.000      7.640      2.
960
    Left Subcortical Box Tissue     44.809     47.190      5.
390
       Left Subcortical Box CSF      0.000      4.750      1.
950
   Right Subcortical Box Tissue     43.473     48.170      5.
480
      Right Subcortical Box CSF      0.000      5.190      2.
010
      Left Brainstem Box Tissue     18.380     16.210      2.
520
         Left Brainstem Box CSF      0.000      3.930      1.
860
     Right Brainstem Box Tissue     16.531     17.020      2.
650
        Right Brainstem Box CSF      0.000      4.190      1.
990
    Left Ventricle-2 Box Tissue     59.649     60.690      7.
740
       Left Ventricle-2 Box CSF      0.000      7.850      4.
550
   Right Ventricle-2 Box Tissue     58.947     62.880      7.
800
      Right Ventricle-2 Box CSF      0.000      7.700      4.
380
      Left Ventricle Box Tissue    110.283    119.590     13.
390
         Left Ventricle Box CSF      0.000      9.430      5.
280
     Right Ventricle Box Tissue    107.108    122.980     13.
710
        Right Ventricle Box CSF      0.000      9.510      5.
180



-- 
Christoph Christmann                  christma at as200.zi-mannheim.de
Psychologist, MEE                     Fon/Fax +49 621 1703 63 18/05
Central Institute of Mental Health    http://www.zi-mannheim.de
Department of Neuropsychology         D-68159 Mannheim J5
and Clinical Psychology                

****************************************************************************
******************
IMPORTANT: The contents of this email and any attachments are confidential.
They are intended for the 
named recipient(s) only.
If you have received this email in error, please notify the system manager
or the sender immediately and do 
not disclose the contents to anyone or make copies thereof.
*** eSafe scanned this email for viruses, vandals, and malicious content.
***
****************************************************************************
******************

_______________________________________________
Brains-users mailing list
Brains-users at www.psychiatry.uiowa.edu
http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users