[Brains-users] segmentation measurement
Ronald Pierson
ronald-pierson at uiowa.edu
Mon Jan 30 21:26:33 PST 2006
Cygwin documentations sounds great. This forum is certainly open for all
those topics. For instance, the cutting of the brainstem at the point we
chose is rather subjective, and I think there is a fair amount of
variability. Luckily, the brainstem box really is not used for any research
- I don't know of anyone who is interested in brainstem tissue volumes (!).
An alternative would be to load the Talairach parameters, and display them
as a grid. That will show the two rows of boxes that we include for the
cerebellum at the bottom. Just cut off the brainstem/spinal cord at the
lower limit of this expanded Talairach grid, and there is no more
subjectivity!
Ron
-----Original Message-----
From: Christoph Christmann [mailto:christma at zi-mannheim.de]
Sent: Monday, January 30, 2006 7:51 AM
To: Ronald Pierson; brains-users at psychiatry.uiowa.edu
Subject: RE: [Brains-users] segmentation measurement
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.
>***************************************************************************
*
>******************
>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
--
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.
***
****************************************************************************
******************
More information about the Brains-users
mailing list