[Brains-users] segmentation measurement

[Ronald Pierson]

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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