[Brains-users] segmentation measurement
Christoph Christmann
christma at zi-mannheim.de
Mon Jan 30 05:51:18 PST 2006
Hi Ron, hi Eugene,
I got everything (except the zeros for the CSF in the T50 algorithm)
working now!
Many thanks again for the support! Our MD student started this
morning and I could provide her a running system - great!
I will now write a short Script about installing and using Brains2
under Cygwin and Suse 9.3 in German. If anyone is insterested or
would like to participate I would be glad to get an email.
BTW: Is it possible to discuss other topics like automatic algorithms
for SNR measurement or individual segmentation strategies in this
list? For example, I would like to learn and discuss about advantages
or disadvantages of cutting the brainstem at a certain point,
defining parts of the anterior cingulate cortex etc.
Best regards
Christoph
At Friday 27.01.2006 18:33, Ronald Pierson wrote:
>This one is a frustrating carry-over from how the discrete image is
>generated. Try saving the Talairach parameters in the 10_ACPC as
>Talairach.bnd.
>
>You have named your Talairach bounds something different from what it
>expects. During the measurement of seg vols you have specified that name,
>and that is loaded for use in creating Talairach boxes, masks of the lobes,
>etc. However, when the discrete image is created, it is called with a
>command that doesn't assume you have any Talairach bounds loaded, and
>doesn't check. Bummer. So, it goes out and looks for the default name for
>Talairach bounds in the 10_ACPC directory, and if it fails to find it, it
>doesn't stop. It just goes on and tries to measure that image. Since that
>image wasn't created, it has many errors, etc.
>
>Let me know if this doesn't fix it.
>
>Ron
>
>
>-----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: Friday, January 27, 2006 11:23 AM
>To: brains-users at psychiatry.uiowa.edu
>Subject: [Brains-users] segmentation measurement
>
>Dear Eugene, dear Ronald,
>
>while the error with the CSF volume in the T50 segmentation
>step persists there is a additional error in my workup
>measure segmentation volumes processing. Possibly I missed
>to place something somewhere. Maybe you could have a look at
>the terminal copy below. BTW the kappa values were excellent
>and the segmentation was good!
>
>Thanks and have a nice weekend!
>
>Christoph
>
>-snip------------------------
>
>brains2% cd standard
>brains2% pwd
>/home/morpho/cc/Pat7/Pat7_10_ACPC/standard
>brains2% b2 load image /home/morpho/cc/Pat7/Pat7_10_ACPC/
>Pat7_10_segment.hdr
>Object loaded with filter: strictAnalyze75
>b2 load talairach-parameters /home/morpho/cc/Pat7/
>Pat7_10_ACPC/Pat7_Talairach.bnd
>Object loaded with filter: brains2
>b2 load mask /home/morpho/cc/Pat7/Pat7_10_ACPC/
>Pat7_brain_cut_clean.mask
>Object loaded with filter: brains2
>b2 threshold image i3 70
>b2 and masks m4 m3
>b2 fill internal mask m5
>b2 and masks m3 m6
>b2 split mask m3 x 140 left
>b2 split mask m3 x 140 right
>b2 split mask m7 x 140 left
>b2 split mask m7 x 140 right
>b2 destroy mask m7
>b2 destroy mask m5
>b2 destroy mask m4
>b2 destroy mask m6
>Notice: no talairach parameters found (tried brains2, then
>brains).
>Object "-1" not found in function GetObjectPointer, file /
>scratch/hjohnson/src/brains2/src/iplObject/
>b2GUIObjectTableBase.cxx, line 55
>Valid Objects with prefix 'i' are: i1 i2 i3
>
>SIMPLE_ERROR: Error: Invalid image object specified in b2
>threshold image.
>Object "-1" not found in function GetObjectPointer, file /
>scratch/hjohnson/src/brains2/src/iplObject/
>b2GUIObjectTableBase.cxx, line 55
>Valid Objects with prefix 'm' are: m1 m10 m11 m2 m3 m8 m9
>
>-snip-
>
>Object "-1" not found in function DestroyObjectPointer, file
>/scratch/hjohnson/src/brains2/src/iplObject/
>b2GUIObjectTableBase.cxx, line 152
>b2 measure class-volume mask m8 i3
>brains2(bk_classVolumeMask) version 2005-07-27 for cc Pat7
>at Fri_Jan_27_17:59:09_2006 using Pat7_10_segment.hdr
>created by morpho for l_brain traced by gave:
> GM-Volume: 293.980307 cubic centimeters
> WM-Volume: 177.736029 cubic centimeters
> CSF-Volume: 62.017494 cubic centimeters
> VB-Volume: 1.779891 cubic centimeters
> Other-Volume: 0.101618 cubic centimeters
>b2 measure class-volume mask m9 i3
>brains2(bk_classVolumeMask) version 2005-07-27 for cc Pat7
>at Fri_Jan_27_17:59:09_2006 using Pat7_10_segment.hdr
>created by morpho for r_brain traced by gave:
> GM-Volume: 297.081289 cubic centimeters
> WM-Volume: 177.892926 cubic centimeters
> CSF-Volume: 64.810618 cubic centimeters
> VB-Volume: 2.162270 cubic centimeters
> Other-Volume: 0.062857 cubic centimeters
>b2 measure class-volume mask m10 i3
>brains2(bk_classVolumeMask) version 2005-07-27 for cc Pat7
>at Fri_Jan_27_17:59:10_2006 using Pat7_10_segment.hdr
>created by morpho for l_intCSF_brain traced by gave:
> GM-Volume: 289.459978 cubic centimeters
> WM-Volume: 177.736029 cubic centimeters
> CSF-Volume: 46.075880 cubic centimeters
> VB-Volume: 0.625424 cubic centimeters
> Other-Volume: 0.059714 cubic centimeters
>b2 measure class-volume mask m11 i3
>brains2(bk_classVolumeMask) version 2005-07-27 for cc Pat7
>at Fri_Jan_27_17:59:10_2006 using Pat7_10_segment.hdr
>created by morpho for r_intCSF_brain traced by gave:
> GM-Volume: 292.317932 cubic centimeters
> WM-Volume: 177.892926 cubic centimeters
> CSF-Volume: 48.401752 cubic centimeters
> VB-Volume: 1.223610 cubic centimeters
> Other-Volume: 0.029333 cubic centimeters
>
>-snip-
>
>I end up with zero volumes in the tabel for all volumes.
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--
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
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