Brainvisa T1 pipeline problem

keepmoon · Post by **keepmoon** » Wed Nov 11, 2009 2:45 pm

Hello everyone,

I am a beginner for brainvisa. Now I am just following brainmanual to test what it can do.
I have already done: (1) add a database. (2) Import a T1 MRI.(3) prepare subject for anatomical pipeline.
But for Ana Do A Lot of Thing from T1MRI (T1 MRISegmentation pipelineT1 Pipeline 2007), when I run it, there is an error. I search in this forum and didn’t find similar problem /answer. Anyone can help me? Thank you very much!

Li

Error information:
-----------------------------
! VIP Warning:
Different Xvoxsize ans Yvoxsize in Compute3DNorm!
------------------------------
------------------------------
! VIP Warning:
Different Xvoxsize ans Yvoxsize in Extract3DExtrema!
------------------------------
------------------------------
! VIP Warning:
Strange: gap of more than 5 points along this trajectory (use smaller scale step)
------------------------------
Singularity steming from iteration 1375 and localization 26
lost at iteration 0
------------------------------
! VIP Warning:
Strange: gap of more than 5 points along this trajectory (use smaller scale step)
------------------------------
Singularity steming from iteration 218 and localization 23
lost at iteration 0
------------------------------
!! VIP Error:
Uncomplete infinite family:
------------------------------
No minimum of second derivative trajectory
------------------------------
!! VIP Error:
Execution aborted in function 'VipCreateHighestCascade'.
------------------------------
------------------------------
!! VIP Error:
Sorry, the analysis can not proceed further
------------------------------

in Vip Histogram analysis 1 System command exited with non null value : 111

RuntimeError
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (73) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'y', '-m', 'a', '-u', self.undersampling )
neuroProcessesGUI.py (1294) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2051) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

in Histogram analysis 1 System command exited with non null value : 111

RuntimeError
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
neuroProcesses.py (754) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1733) in _run:
return node.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1559) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1805) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (73) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'y', '-m', 'a', '-u', self.undersampling )
neuroProcessesGUI.py (1294) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2051) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

in T1 Pipeline 2007 1 System command exited with non null value : 111

RuntimeError
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
neuroProcesses.py (754) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1626) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1559) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1805) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
neuroProcesses.py (754) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1733) in _run:
return node.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1559) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1805) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (73) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'y', '-m', 'a', '-u', self.undersampling )
neuroProcessesGUI.py (1294) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2051) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

Process T1 Pipeline 2007 1 finished on 2009/11/11 13:51 (3 minutes 3 seconds)

Post by **Dominique Geffroy** » Fri Nov 27, 2009 2:29 pm

Hi,

Maybe there was a problem with the previous step, bias correction. You can try the alternative method for this step or for the histogram analysis step, or try to decrease the field rigidity in bias correction step.
You can find some explainations here : http://brainvisa.info/doc/brainvisa-3.2 ... ction.html

Dominique

keepmoon · Post by **keepmoon** » Mon Nov 30, 2009 5:08 pm

Dominique Geffroy wrote:Hi,

Maybe there was a problem with the previous step, bias correction. You can try the alternative method for this step or for the histogram analysis step, or try to decrease the field rigidity in bias correction step.
You can find some explainations here : http://brainvisa.info/doc/brainvisa-3.2 ... ction.html

Dominique

Dear Dominique,

Thank you very much for your reply! I will have a look!

Li

sebastian · Post by **sebastian** » Tue Dec 01, 2009 12:22 pm

Dear keepmoon,

I know this problem. May be the x and y size are different (exemple : xsize = 0.9375 and ysize = 0.9374999999). If I'm correct you have to edit the yourimage.ima.minf and may be yourimage.dim to get exact xsize and ysize and let the pipeline do the whole process without any error. Use the AimsFileInfo command to know the dimensions of the T1 image (or in anatomist). Let me know the results of "AimsFileInfo yourimage.ima" to be more specific about your problem. This method may correct the following error message : "Different Xvoxsize ans Yvoxsize in Compute3DNorm". For the other error messages you have to first correct X and Y size relaunch the process and see wich error survive.

Best regards

Sebastian

keepmoon · Post by **keepmoon** » Fri Dec 04, 2009 5:22 pm

Dear Sebastian,

Thank you very much for your help! I run brainvisa on Windows Xp, so maybe can't type the command "AimsFileInfo". But I sue MRICRON to check the origin data. It is true that x, y size are not the same (x: 1.2100, y: 1.0001). So I change x,y,z into the same size. Then run the data again. This time the error "Different Xvoxsize ans Yvoxsize in Compute3DNorm" is solved. But remanding errors are still.
I think maybe there are something wrong with previous steps. Especially in this step "Prepare Subject for Anatomical Pipeline", for the option of "Anterior_Commissure, Posterior_Commisure, Interhemispheric_Point, Left_Hemisphere_Point", I don't know how to do. I see some instruction say: Click on that open button of the Anterior_commissure parameter. Antomist must load the T1 MRI. It is truely that there are two windows pop up. maybe now I need to do somthing. the anatomist will report the coordirate of Anterior_Commissure, Posterior_Commisure, Interhemispheric_Point, Left_Hemisphere_Point to the brain visa. I don't know how to process this step. I just press any place randly. then there are coordirate pop up in the blank of Anterior_Commissure. I don't know this process whether is right. But this step can run. Untill next step "Ana Do A Lot of Thing from TI MRI" , there are following errors.
If you or someone have detailed process step instruction, can share with me? I am appreciated for any help!

Process T1 Pipeline 2007 2 started on 2009/12/04 16:46
OK, the image seems to be in the correct orientation.
------------------------------
! VIP Warning:
Strange: gap of more than 5 points along this trajectory (use smaller scale step)
------------------------------
Singularity steming from iteration 1415 and localization 26
lost at iteration 0
------------------------------
! VIP Warning:
Strange: gap of more than 5 points along this trajectory (use smaller scale step)
------------------------------
Singularity steming from iteration 218 and localization 23
lost at iteration 0
------------------------------
!! VIP Error:
Uncomplete infinite family:
------------------------------
No minimum of second derivative trajectory
------------------------------
!! VIP Error:
Execution aborted in function 'VipCreateHighestCascade'.
------------------------------
------------------------------
!! VIP Error:
Sorry, the analysis can not proceed further
------------------------------

in Vip Histogram analysis 2 System command exited with non null value : 111

RuntimeError
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (73) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'y', '-m', 'a', '-u', self.undersampling )
neuroProcessesGUI.py (1294) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2051) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

in Histogram analysis 2 System command exited with non null value : 111

RuntimeError
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
neuroProcesses.py (754) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1733) in _run:
return node.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1559) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1805) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (73) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'y', '-m', 'a', '-u', self.undersampling )
neuroProcessesGUI.py (1294) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2051) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

in T1 Pipeline 2007 2 System command exited with non null value : 111

RuntimeError
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
neuroProcesses.py (754) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1626) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1559) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1805) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
neuroProcesses.py (754) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1733) in _run:
return node.run( context )
neuroProcesses.py (1441) in run:
return self._run( context )
neuroProcesses.py (1559) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1805) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1960) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (73) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'y', '-m', 'a', '-u', self.undersampling )
neuroProcessesGUI.py (1294) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2051) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

sebastian · Post by **sebastian** » Sat Dec 05, 2009 12:31 am

Dear Keepmoon,

xsize and ysize are quiet different here (1.21 vs 1.0001) you may reslice your image to get the same value for both dimensions (x & y). To do so, switch to "expert" user level (BrainVisa menu > preferences > userLevel and choose "expert") and relaunch brainvisa (optional). Find the resampling tool in "Tools" > "registration" and the double-click on "Resampling" : pick up your image in "image_input" and choose a filename for the resampled image in "image_output", example " /whatever/yourimage.ima", leave all the remaining fields empty except sizeX and sizeY set to 1 for each. This process will resample x and y dimensions, the motion field is set by default to "identity". You could then create a new patient by importing to the database the resampled image. I will ask to Brainvisa guru to let x & y different dimensions images valid for this great pipeline. For the first step, you need to see this page http://brainvisa.info/doc/brainvisa-3.2 ... bject.html
For the remaining error messages let me know how it works after the additional resampling step ("Resampling" tool) and a right "prepare subject ...".

Best regards

Sebastian

Post by **riviere** » Sat Dec 05, 2009 12:54 am

Hi,
Thanks for the explanation, Sebastian!
I'm not really sure the voxels size is really the cause of the problem, it should be only a warning, and resampling may bring aditional partial volume problems, but you can try...
If it doesn't help, trying different bias correction parameters as Dominique suggests might solve the problem.
Denis

sebastian · Post by **sebastian** » Sat Dec 05, 2009 1:03 am

Dear Keepmoon, dear Denis,

I'm wrong ! "Resampling" needs size and dim to be set. If you set 1 for sizex you need to set dimx according to the initial dimensions of the image. For example : size x equal 2 mm and dim x 256 if you want to resample size x to 1 mm you must set dim x to 512.

Best regards

Sebastian

keepmoon · Post by **keepmoon** » Mon Dec 07, 2009 5:44 pm

Dear everyone,
Thank you very much for the help of all. Today I change another data to run. It can run sucessfully for this step “T1 pipeline 2007” with this warning information. maybe somewhere is also wrong! In fact, these two images look like similar, but this image can run all the steps with little error.

Left hemisphere point not specified - X axis flip will not be checked“OK, the image seems to be in the correct orientation.
------------------------------
! VIP Warning:
Different Xvoxsize ans Yvoxsize in Compute3DNorm!
------------------------------
------------------------------
! VIP Warning:
Different Xvoxsize ans Yvoxsize in Extract3DExtrema! ------------------------------
Computing left hemisphere grey-white classification...
Computing right hemisphere grey-white classification...

New cubic spatial resolution:0.943588”…..

Post by **Dominique Geffroy** » Tue Dec 08, 2009 9:33 am

Hi,

the first message appears because you didn't enter the coordinates of a left hemisphere point in Prepare subject step. It is not mandatory but if don't give this parameter the orientation of the image cannot be check according to left to right axis. Be carreful when you select a point on the left: Anatomist displays image in radiological convention by default (left and right inverted).

Maybe the other messages are not very important. You should check the resulting images: brain mask, split mask, hemisphere meshes and so on. If there are correct, don't matter about the warnings.

Dominique

keepmoon · Post by **keepmoon** » Tue Dec 08, 2009 5:01 pm

Dear Dominique Geffroy,

In fact, in this Stepp „Prepare Subject for Anatomical Pipeline“ I have already chose these four coordinates (although I don’t know whether it is right) for AC, PC, IP and LHP. But when I do the next step “Ana Do A Lot of Thing from TI MRI”, It just shows the first three points coordinates without the coordinate of LHP. Moreover, when I choose the coordinates, you say “Anatomist displays image”, but here I just can see a red cross in the windows of the anatomist without any brain image. Maybe there are something wrong with my software.
Today I read some tutorial for this software. It says that user interface consists of three parts (1,menu; 2, a window providing access to processes; 3, a window providing information on the selected process). But in my computer, I just have the first two parts without “a window providing information on the selected process” part.
Today I also change a new version 3.2.0 to have a try. The user interface of this version can show all these three parts, But also with other error. I follow the instruction: first step, create a databases; then Import T1 MRI. For this step it shows some error (as following). But for version 3.1 it can run successfully for this step.
I will be appreciated for any help!

in Import T1 MRI 3 Cannot find out in which database "Z:\Mitarbeiter\kongli\my file\brainvisa-test\subj\0484\t1mri\default_acquisition\0484.referential" should be inserted

NotInDatabaseError
neuroProcesses.py (1811) in _processExecution: result = process.execution( self )
ImportT1MRI.py (186) in execution:
ref = tm.createNewReferentialFor( self.output, name='Raw T1 MRI' )
registration.py (423) in createNewReferentialFor:
self.__databases.insertDiskItem( referential, update=True )
sqlFSODatabase.py (151) in insertDiskItem:
self.insertDiskItems( ( item, ), **kwargs )
sqlFSODatabase.py (1291) in insertDiskItems:
raise Database.NotInDatabaseError( _( 'Cannot find out in which database "%s" should be inserted' ) % ( diskItem.fullPath(), ) )

Post by **Dominique Geffroy** » Tue Dec 08, 2009 6:07 pm

You says you don't see the mri image in Anatomist window ?! So how did you select the AC, PC points ? I'm not sure I understand what you've done...
If you can't visualize images, maybe it is a problem of graphical card driver.
What system do you use ? Windows ?
Could you send screen copy to show the problem or the log file of brainvisa ?

keepmoon · Post by **keepmoon** » Wed Dec 09, 2009 3:33 pm

Dear Dominique Geffroy ,

I am using Windows Xp and brainvisa3.1 for analysis data (*.img/*.hdr). When I choose the AC coordidate, I press the button on the right place of Anterior_commisure blank for the first time, it will pop up two anatomist windows (in brainvisa manual, it shows thiere is a brainand a cross in that small window, but in my computer just show a red cross without brain). then I press that button again. A coordinate will shows on the Anterior_commisure blank. By the same way, I choose the pc,Ihp, Lhp coordinates.
I am sorry I don't know how to put this screen copy here. So I just put the content of log here. I am appreciated for your help!

The log:

<?xml version="1.0" encoding="utf-8" ?>
<minf expander="brainvisa-log_2.0">
<f type="LogFile.Item">
<s name="what">Read processes</s>
<s name="html">processesPath = ['C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\processes']</s>
<n name="when">1260365959.43</n>
<f type="LogFileLink" name="children">
<s>C:\Temp\bv_28200</s>
</f>
<s name="icon">icon_process.png</s>
</f>
<f type="LogFile.Item">
<s name="what">starting BrainVISA</s>
<s name="html"><html><body><h1>BrainVISA 3.1</h1>
<h2>Python version</h2>2.5.4 (r254:67916, Dec 23 2008, 15:10:54) [MSC v.1310 32 bit (Intel)]
<h2>Command line</h2>
<tt>"C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\brainvisa"</tt>
<h2>Environment variables</h2><tt>TMP = C:\Temp</tt><tt>COMPUTERNAME = W1072519</tt><tt>EA = 001635A72168</tt><tt>PEPXL = L:\PEP</tt><tt>USERDOMAIN = KHD</tt><tt>HLS_IPADDR = 161.42.182.120</tt><tt>DEFLOGDIR = c:\WINNT\Profiles\All Users\Anwendungsdaten\McAfee\DesktopProtection</tt><tt>COMMONPROGRAMFILES = C:\Programme\Gemeinsame Dateien</tt><tt>PROCESSOR_IDENTIFIER = x86 Family 15 Model 4 Stepping 3, GenuineIntel</tt><tt>PROGRAMFILES = C:\Programme</tt><tt>PROCESSOR_REVISION = 0403</tt><tt>SYSTEMROOT = C:\WINNT</tt><tt>PATH = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\bin\commands-links;C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib;C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python;C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python\DLLs;C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\bin;C:\WINNT\system32;C:\WINNT;C:\WINNT\System32\Wbem;c:\Programme\QuickTime\QTSystem\;C:\Programme\Windows Imaging\;c:\standa~1\s-plan;C:\Programme\MATLAB701\bin\win32;C:\Programme\MATLAB\R2009a\bin;C:\Programme\MATLAB\R2009a\bin\win32</tt><tt>LANGUAGE = en</tt><tt>HL_SEARCH = 378p,IP,IPX</tt><tt>TK_LIBRARY = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python\tcl\tk8.4</tt><tt>DCMDICTPATH = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\dicom.dic</tt><tt>PROCESSOR_ARCHITECTURE = x86</tt><tt>SHFJ_SHARED_PATH = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\share</tt><tt>TIX_LIBRARY = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python\tcl\tix8.4</tt><tt>ALLUSERSPROFILE = C:\WINNT\Profiles\All Users</tt><tt>SARA_BASE_NT = C:\WINNT\system32\drivers</tt><tt>SESSIONNAME = Console</tt><tt>HOMEPATH = \KongLi</tt><tt>UATDATA = C:\WINNT\system32\CCM\UATData\D9F8C395-CAB8-491d-B8AC-179A1FE1BE77</tt><tt>USERNAME = kongli</tt><tt>LOGONSERVER = \\ADS01</tt><tt>PROMPT = $P$G</tt><tt>COMSPEC = C:\WINNT\system32\cmd.exe</tt><tt>QTJAVA = c:\Programme\QuickTime\QTSystem\QTJava.zip</tt><tt>PYTHONPATH = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\python;C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python\Lib\site-packages;C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python\Lib\site-packages\win32;C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python\Lib\site-packages\win32\lib</tt><tt>CLASSPATH = .;c:\Programme\QuickTime\QTSystem\QTJava.zip</tt><tt>TCL_LIBRARY = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python\tcl\tcl8.4</tt><tt>VSEDEFLOGDIR = c:\WINNT\Profiles\All Users\Anwendungsdaten\McAfee\DesktopProtection</tt><tt>HOMESHARE = \\BAS30\PSYCH-Basis</tt><tt>PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH</tt><tt>CLIENTNAME = Console</tt><tt>FP_NO_HOST_CHECK = NO</tt><tt>WINDIR = C:\WINNT</tt><tt>TEMP = C:\Temp</tt><tt>HOMEDRIVE = N:</tt><tt>SYSTEMDRIVE = C:</tt><tt>PYTHONHOME = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\lib\python</tt><tt>NUMBER_OF_PROCESSORS = 1</tt><tt>APPDATA = N:\KongLi\Einstellungen</tt><tt>USERDNSDOMAIN = ADS.KRZ.UNI-HEIDELBERG.DE</tt><tt>PROCESSOR_LEVEL = 15</tt><tt>OS = Windows_NT</tt><tt>OEKURZ = PSYCH</tt><tt>USERPROFILE = C:\WINNT\Profiles\kongli</tt><h2>BrainVISA options</h2><code>platform = windows</code><code>gui = True</code><code>sessionID = bba9d9b5-c430-03f9-fd4b-07d66c68a967</code><code>userProfile = None</code><code>siteOptionFile = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\brainvisa\options.minf</code><code>userOptionFile = C:\WINNT\Profiles\kongli\.brainvisa\options.minf</code><code>logFileName = C:\WINNT\Profiles\kongli\.brainvisa\brainvisa4.log</code><code>temporaryDirectory = C:\Temp</code><code>mainPath = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\brainvisa</code><code>iconPath = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\share\brainvisa-3.1\icons</code><code>typesPath = ['C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\types', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\brainrat\\types', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\connectomist\\types', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\cortical_surface\\types', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\morphometry\\types', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\structural_analysis\\types', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\sulci\\types', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\t1mri\\types']</code><code>dataPath = [<brainvisa.configuration.databases_configuration.DatabaseSettings object at 0x0B5C6C10>]</code><code>processesPath = ['C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\processes']</code><code>fileSystemOntologiesPath = ['C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\hierarchies', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\connectomist\\hierarchies', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\cortical_surface\\hierarchies', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\structural_analysis\\hierarchies', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\sulci\\hierarchies', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\toolboxes\\t1mri\\hierarchies']</code><code>mainDocPath = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\share\doc\brainvisa-3.1</code><code>docPath = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\bin\..\share\doc\brainvisa-3.1\en</code><code>anatomistExecutable = anatomist</code><code>matlabRelease = None</code><code>matlabExecutable = matlab</code><code>matlabOptions = -nosplash -nojvm</code><code>matlabPath = ['C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\matlab', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\matlab\\utils', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\matlab\\mesh', 'C:\\Programme\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\brainvisa\\matlab\\LoadSave']</code><code>matlabStartup = []</code><code>spmDirectory = </code><code>logFileName = C:\WINNT\Profiles\kongli\.brainvisa\brainvisa4.log</code><code>language = en</code><code>userLevel = 0</code><code>startup = ["execfile('C:\\\\Programme\\\\cartopack-Windows-XP-i686-3.1.6-2009_05_14\\\\brainvisa\\\\startup.py',globals(),{})"]</code><code>supportEmail = support@brainvisa.info</code><code>SMTP_server_name = localhost</code><code>flatHierarchy = C:\Programme\cartopack-Windows-XP-i686-3.1.6-2009_05_14\brainvisa\shfjFlatHierarchy.py</code><code>textEditor = notepad</code><code>removeTemporary = True</code></body></html></s>
<n name="when">1260365959.43</n>
<s name="icon">brainvisa_small.png</s>
</f>
<f type="LogFile.Item">
<s name="what">Import T1 MRI 1</s>
<f type="TextFileLink" name="html">
<s>C:\Temp\bv_28202</s>
</f>
<n name="when">1260366348.88</n>
<f type="LogFileLink" name="children">
<s>C:\Temp\bv_28201</s>
</f>
<s name="icon">icon_process.png</s>
</f>
<f type="LogFile.Item">
<s name="what">Anatomist </s>
<f type="TextFileLink" name="html">
<s>C:\Temp\bv_28209</s>
</f>
<n name="when">1260366501.38</n>
<l length="1" name="children">
<f type="LogFile.Item">
<s name="what">Communications</s>
<f type="TextFileLink" name="html">
<s>C:\Temp\bv_28208</s>
</f>
<n name="when">1260366501.38</n>
</f>
</l>
<s name="icon">anaIcon_small.png</s>
</f>
<f type="LogFile.Item">
<s name="what">Prepare Subject for Anatomical Pipeline 1</s>
<f type="TextFileLink" name="html">
<s>C:\Temp\bv_282011</s>
</f>
<n name="when">1260368568.75</n>
<f type="LogFileLink" name="children">
<s>C:\Temp\bv_282010</s>
</f>
<s name="icon">icon_process.png</s>
</f>
<f type="LogFile.Item">
<s name="what">T1 Pipeline 2007 1</s>
<f type="TextFileLink" name="html">
<s>C:\Temp\bv_282014</s>
</f>
<n name="when">1260368643.18</n>
<f type="LogFileLink" name="children">
<s>C:\Temp\bv_282013</s>
</f>
<s name="icon">icon_process.png</s>
</f>

Post by **riviere** » Thu Dec 10, 2009 1:51 am

Hi,

I haven't really looked at your log, but from what you described, it seems that OpenGL does not work correctly on your machine.
In XP, with some 3D cards, you can decrease the level of 3D hardware acceleration. I don't exactly remember where, it's somewhere in the display properties (right-click on the desktop background), then in some sort of "expert settings". It sometimes helps because OpenGL bugs are generally in 3D hardware drivers (we have seen such phenomenons on many many cheap 3D Intel chipsets).
However in a few cases it just doesn't help... in this situation I cannot provide any other advice than "switch to another machine with a 'real' 3D card", or to Linux...

By the way we never mentioned it but in the Linux package of BrainVisa 3.2, we have shipped a software OpenGL library (the standard Mesa lib), which is not used by default because the system OpenGL is generally way faster if it works, but in case of 3D problems it is possible to use it instead of the system one: just move (or copy, or symlink) the <cartopack...>/lib/mesa/* files one folder up, to <cartopack...>/lib/
I have not suceeded (yet?) in building a working Mesa OpenGL lib on Windows, so we could not provide the same solution for Windows.

Denis

Post by **Dominique Geffroy** » Thu Dec 10, 2009 9:43 am

Indeed, as Denis said you have to solve this display problem to be able to use Brainvisa T1 pipeline.
For the step where you choose the AC, PC coordinates, you need to see the brain image because you have to click on the correct point before reporting its coordinate by clicking again on the button near the field anterior commissure. If you don't know how to place the points, you have a video in Brainvisa tutorial that might help you : http://brainvisa.info/doc/brainvisa-3.2 ... re_subject

BrainVISA

Brainvisa T1 pipeline problem

Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem

Re: Brainvisa T1 pipeline problem