Dear Dominique Geffroy and riviere,
Thank you very much for your help! Following your advice I change another computer and it can show the image when choose the coordinates of AC and PC. But I also met some problems.
(1) when doing the step import T1 MRI, There is an option: “input_spm_orientation” and it has two options: Neurological and radiological. In the brainvisamanual, it chooses Not applicable. But here without this option.
(2) When I do the step: prepare subject for anatomical pipeline1, For choosing the coordinates of AC, PC, When I press the button , it will pop up two anatomist windows. But my small windows with a yellow line (in the manual of brainvisa is a red line), I know that different lines represent different coordinate systerms. When I choose the coordinates of AC, PC, should I change the yellow line into red line? (In this test I change it into red line and choose the coordinates of AC,PC, IHP and LHP following the manual).
(3) In this step, When I input the data, it just pop up automatically the coordinates of AC, PC, IHP, without the coordinate of LHP(??)
when I run this step, it will pop up following warning:
Left hemisphere point not specified - X axis flip will not be checked (Maybe because above step without the coordinate of LH , there is this warning here)
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:0.94545
Computing oversampled MR image to improve cortical surface definition (cubic spline)
Computing oversampled voronoi diagram (nearest neighbor)
Masking Bias corrected image with left hemisphere mask...
Detecting left grey/white interface...
I don’t know whether I describe my problem clearly? If not, I can send the steps of this process with pictures to your email. Here I don’t know how to upload an attach. I am appreciated for your help!
Best regards!
Li
Brainvisa T1 pipeline problem
-
riviere
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Re: Brainvisa T1 pipeline problem
Hi,
If the colored bar on the 3D window is not red, that means that the displayed object (the MRI) already has a referential assigned, yes. For the AC/PC coordinates, they will be transformed and used by BrainVisa in this MRI own coordinates system (whatever it is), so it doesn't matter which referential you are using for visualization (as long as it has a transformation to the MRI space).
It's generally more comfortable for users to view a MRI in its own coordinates system (yellow here) so you'd better not change it, but it's just for user feeling...
Denis
If the colored bar on the 3D window is not red, that means that the displayed object (the MRI) already has a referential assigned, yes. For the AC/PC coordinates, they will be transformed and used by BrainVisa in this MRI own coordinates system (whatever it is), so it doesn't matter which referential you are using for visualization (as long as it has a transformation to the MRI space).
It's generally more comfortable for users to view a MRI in its own coordinates system (yellow here) so you'd better not change it, but it's just for user feeling...
just means that you have not filled the optional "left_hemisphoere_point" parameter and so the process is not able to check for a X-axis flip. In most cases it is OK.Left hemisphere point not specified - X axis flip will not be checked
Denis
Re: Brainvisa T1 pipeline problem
Dear riviere,
Thank you very much for your help!
Thank you very much for your help!
Re: Brainvisa T1 pipeline problem
Hello,
I have a somewhat related problem on some of the workstations we are using here. We are running brainvisa 3.2 on a linux server to which we access usinf XP or Unix workstations. On *some* of these latter, we cannot select the AC, PC, IH points because, because anatomist does not load the image automatically: Clicking the 'eye'; logo from the process GUI next to the AC, PC, IH selection boxes launches Anatomist but the images are not loaded. Loading the images manually from anatomist disply the images properly but then the coordinates of the points are not updated in the corresponding text boxes (I think the only coordinates tha show up are those from the center of the image volume).
thanks for your help.
- Sylvain.
I have a somewhat related problem on some of the workstations we are using here. We are running brainvisa 3.2 on a linux server to which we access usinf XP or Unix workstations. On *some* of these latter, we cannot select the AC, PC, IH points because, because anatomist does not load the image automatically: Clicking the 'eye'; logo from the process GUI next to the AC, PC, IH selection boxes launches Anatomist but the images are not loaded. Loading the images manually from anatomist disply the images properly but then the coordinates of the points are not updated in the corresponding text boxes (I think the only coordinates tha show up are those from the center of the image volume).
thanks for your help.
- Sylvain.
-Sylvain.
-
riviere
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Re: Brainvisa T1 pipeline problem
Hi Sylvain,
You mean you are using a X server on Windows, and use BrainVisa/Anatomist remotely from a linux server, displaying on windows ?
I must admit that we have never tried this kind of configuration.
If it *sometimes works*, then there should be a good reason if it sometimes does not...
First, if you have a large database (about 100 subjects or more), the first time brainvisa loads a data in anatomist, it takes time because the coordinates referenetials/transformation is not optimized (yet) and has to be loaded entirely in brainvisa, and it may seem to do nothing for a minute or so, and after that things are correctly done.
Then, does it work better if the same operations are done, triggered and displaying on a linux machine ?
Is there any kind of error message in the log (maybe in the "anatomist communication" messages) ?
Remote display of 3D OpenGL scenes is subject to bugs, even between linux machines, so I really don't know what may occur when run on a X server on a Windows machine. However if it just does nothing, and if objects are not even loaded in anatomist, I suspect more a socket communication error or hangup than a 3D display problem.
But I don't really know right now how to solve that...
Denis
You mean you are using a X server on Windows, and use BrainVisa/Anatomist remotely from a linux server, displaying on windows ?
I must admit that we have never tried this kind of configuration.
If it *sometimes works*, then there should be a good reason if it sometimes does not...
First, if you have a large database (about 100 subjects or more), the first time brainvisa loads a data in anatomist, it takes time because the coordinates referenetials/transformation is not optimized (yet) and has to be loaded entirely in brainvisa, and it may seem to do nothing for a minute or so, and after that things are correctly done.
Then, does it work better if the same operations are done, triggered and displaying on a linux machine ?
Is there any kind of error message in the log (maybe in the "anatomist communication" messages) ?
Remote display of 3D OpenGL scenes is subject to bugs, even between linux machines, so I really don't know what may occur when run on a X server on a Windows machine. However if it just does nothing, and if objects are not even loaded in anatomist, I suspect more a socket communication error or hangup than a 3D display problem.
But I don't really know right now how to solve that...
Denis
Re: Brainvisa T1 pipeline problem
Thank you Denis,
I have looked at the brainvisa log and it says that
- Anatomist has started (indeed, I see Anatomist's main window pop up)
- configuration file is identified: /anatomist/config/settings.cfg
but then, that's it, even waiting several minutes does not help.
The PyAnatomist module does not load,, which would be the next step from what I see on the workstations that actually work well.
Any clue?
I have looked at the brainvisa log and it says that
- Anatomist has started (indeed, I see Anatomist's main window pop up)
- configuration file is identified: /anatomist/config/settings.cfg
but then, that's it, even waiting several minutes does not help.
The PyAnatomist module does not load,, which would be the next step from what I see on the workstations that actually work well.
Any clue?
-Sylvain.
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riviere
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Re: Brainvisa T1 pipeline problem
This may be the key of the problem. Actually, on Linux the pyanatomist module should not be required on anatomist side (just the python client part in BrainVisa), but if it does not load, it clearly indicates that something is not working well. How do you see that the module is not loaded: do you see an error message somewhere ? If you run anatomist alone on the same machine, do you see some abnormal messages ? (you may use the --debugLevel 2 option to see all modules loading logs).The PyAnatomist module does not load,, which would be the next step from what I see on the workstations that actually work well.
Denis
Re: Brainvisa T1 pipeline problem
Thanks again Denis,
when starting anatomist from the command line on this workstation, I see that the config/settings.cfg is loaded and then I see a line specifying that PyAnatomist is present and then a list of modules are loaded. The last message is: all python modules are loaded. It does go that far when anatomist is called from brainvisa, from what I see in the log.
By the way, I have tried anatomist --debugLevel2 and it does not work: the software considers debugLevel2 as a file name. I guess I am typing in the wrong command line.
Sylvain.
when starting anatomist from the command line on this workstation, I see that the config/settings.cfg is loaded and then I see a line specifying that PyAnatomist is present and then a list of modules are loaded. The last message is: all python modules are loaded. It does go that far when anatomist is called from brainvisa, from what I see in the log.
By the way, I have tried anatomist --debugLevel2 and it does not work: the software considers debugLevel2 as a file name. I guess I am typing in the wrong command line.
Sylvain.
-Sylvain.
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riviere
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Re: Brainvisa T1 pipeline problem
Well, then the pyanatomist module seems to be really loaded. What did make you think it was not ?
Then the problem is somewhere else. Maybe a socket communication issue. But I don't really know how to debug it as long as I cannot reproduce the problem.
For the "debugLevel" option, you forgot the space character between "--debugLevel" and "2": 2 is the level of debugging and is the argument to the --debugLevel option. Or if it doesn't work, you may try the "--verbose 2" option instead: actually I don't remember exactly when we introduced the debugLevel option, and before that the verbose option was also used for the verbosity of debug messages. We separated them because it introduced unclear debug messages in applications which actually needed verbosity (like AimsFileInfo -v).
Denis
Then the problem is somewhere else. Maybe a socket communication issue. But I don't really know how to debug it as long as I cannot reproduce the problem.
For the "debugLevel" option, you forgot the space character between "--debugLevel" and "2": 2 is the level of debugging and is the argument to the --debugLevel option. Or if it doesn't work, you may try the "--verbose 2" option instead: actually I don't remember exactly when we introduced the debugLevel option, and before that the verbose option was also used for the verbosity of debug messages. We separated them because it introduced unclear debug messages in applications which actually needed verbosity (like AimsFileInfo -v).
Denis
Re: Brainvisa T1 pipeline problem
Thanks Denis,
the PyAnatomist modules don't launch when anatomist is called form brainvisa. They are launched properly when anatomist is called from the command line.
Here is what I get from launching anatomist with the debugLevel 2. It seems some libraries are not found. But again, it doesn't go that far when called from brainvisa
Any thought on that?
[meg2@megneto ~]$ anatomist --debugLevel 2
Fontconfig warning: line 32: unknown element "cachedir"
Fontconfig warning: line 33: unknown element "cachedir"
Fontconfig error: "conf.d", line 1: no element found
Starting Anatomist.....
libaimsvida.so.3.2.1: libaimsvida.so.3.2.1: cannot open shared object file: No such file or directo
ry
library libaimsvida.so.3.2 successfully loaded.
libaimsdicom.so.3.2.1: libaimsdicom.so.3.2.1: cannot open shared object file: No such file or direc
tory
library libaimsdicom.so.3.2 successfully loaded.
libaimsecat.so.3.2.1: libaimsecat.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsecat.so.3.2 successfully loaded.
libaimsfdf.so.3.2.1: libaimsfdf.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsfdf.so.3.2 successfully loaded.
libaimsjpeg.so.3.2.1: libaimsjpeg.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsjpeg.so.3.2 successfully loaded.
libaimstiff.so.3.2.1: libaimstiff.so.3.2.1: cannot open shared object file: No such file or directory
library libaimstiff.so.3.2 successfully loaded.
libaimsqtformats.so.3.2.1: libaimsqtformats.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsqtformats.so.3.2 successfully loaded.
libaimsminc.so.3.2.1: libaimsminc.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsminc.so.3.2 successfully loaded.
libaimsply.so.3.2.1: libaimsply.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsply.so.3.2 successfully loaded.
libaimsnifti.so.3.2.1: libaimsnifti.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsnifti.so.3.2 successfully loaded.
libaimsgifti.so.3.2.1: libaimsgifti.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsgifti.so.3.2 successfully loaded.
libconnectomist_aims_plugin.so.3.2.1: libconnectomist_aims_plugin.so.3.2.1: cannot open shared object file: No such file or directory
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
config file : /home/meg2/.anatomist/config/settings.cfg
libanafold.so.3.2.1: libanafold.so.3.2.1: cannot open shared object file: No such file or directory
library libanafold.so.3.2 successfully loaded.
libanahistogram.so.3.2.1: libanahistogram.so.3.2.1: cannot open shared object file: No such file or
directory
library libanahistogram.so.3.2 successfully loaded.
libanaprofile.so.3.2.1: libanaprofile.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libanaprofile.so.3.2 successfully loaded.
libanaperfusion.so.3.2.1: libanaperfusion.so.3.2.1: cannot open shared object file: No such file or
directory
library libanaperfusion.so.3.2 successfully loaded.
libanasurfmatch.so.3.2.1: libanasurfmatch.so.3.2.1: cannot open shared object file: No such file or
directory
library libanasurfmatch.so.3.2 successfully loaded.
libanaroibase.so.3.2.1: libanaroibase.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libanaroibase.so.3.2 successfully loaded.
libanaroialgo.so.3.2.1: libanaroialgo.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libanaroialgo.so.3.2 successfully loaded.
libpyanatomistmodule.so.3.2.1: libpyanatomistmodule.so.3.2.1: cannot open shared object file: No su
ch file or directory
PyAnatomist Module present
library libpyanatomistmodule.so.3.2 successfully loaded.
libanavolrender.so.3.2.1: libanavolrender.so.3.2.1: cannot open shared object file: No such file or
directory
library libanavolrender.so.3.2 successfully loaded.
libanavtk.so.3.2.1: libanavtk.so.3.2.1: cannot open shared object file: No such file or directory
library libanavtk.so.3.2 successfully loaded.
libsigraphsvm.so.3.2.1: libsigraphsvm.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libsigraphsvm.so.3.2 successfully loaded.
global modules: /opt/brainvisa/share/anatomist-3.2/python_plugins
home modules: /home/meg2/.anatomist/python_plugins
loading module anacontrolmenu
loading module selection
<H1>Anatomist launched</H1>
loading module volumepalettes
loading module histogram
loading module palettecontrols
loading module modelGraphs
loading module foldsplit
loading module gradientpalette
loading module meshsplit
loading module paletteViewer
all python modules loaded
the PyAnatomist modules don't launch when anatomist is called form brainvisa. They are launched properly when anatomist is called from the command line.
Here is what I get from launching anatomist with the debugLevel 2. It seems some libraries are not found. But again, it doesn't go that far when called from brainvisa
Any thought on that?
[meg2@megneto ~]$ anatomist --debugLevel 2
Fontconfig warning: line 32: unknown element "cachedir"
Fontconfig warning: line 33: unknown element "cachedir"
Fontconfig error: "conf.d", line 1: no element found
Starting Anatomist.....
libaimsvida.so.3.2.1: libaimsvida.so.3.2.1: cannot open shared object file: No such file or directo
ry
library libaimsvida.so.3.2 successfully loaded.
libaimsdicom.so.3.2.1: libaimsdicom.so.3.2.1: cannot open shared object file: No such file or direc
tory
library libaimsdicom.so.3.2 successfully loaded.
libaimsecat.so.3.2.1: libaimsecat.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsecat.so.3.2 successfully loaded.
libaimsfdf.so.3.2.1: libaimsfdf.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsfdf.so.3.2 successfully loaded.
libaimsjpeg.so.3.2.1: libaimsjpeg.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsjpeg.so.3.2 successfully loaded.
libaimstiff.so.3.2.1: libaimstiff.so.3.2.1: cannot open shared object file: No such file or directory
library libaimstiff.so.3.2 successfully loaded.
libaimsqtformats.so.3.2.1: libaimsqtformats.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsqtformats.so.3.2 successfully loaded.
libaimsminc.so.3.2.1: libaimsminc.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsminc.so.3.2 successfully loaded.
libaimsply.so.3.2.1: libaimsply.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsply.so.3.2 successfully loaded.
libaimsnifti.so.3.2.1: libaimsnifti.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsnifti.so.3.2 successfully loaded.
libaimsgifti.so.3.2.1: libaimsgifti.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsgifti.so.3.2 successfully loaded.
libconnectomist_aims_plugin.so.3.2.1: libconnectomist_aims_plugin.so.3.2.1: cannot open shared object file: No such file or directory
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
config file : /home/meg2/.anatomist/config/settings.cfg
libanafold.so.3.2.1: libanafold.so.3.2.1: cannot open shared object file: No such file or directory
library libanafold.so.3.2 successfully loaded.
libanahistogram.so.3.2.1: libanahistogram.so.3.2.1: cannot open shared object file: No such file or
directory
library libanahistogram.so.3.2 successfully loaded.
libanaprofile.so.3.2.1: libanaprofile.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libanaprofile.so.3.2 successfully loaded.
libanaperfusion.so.3.2.1: libanaperfusion.so.3.2.1: cannot open shared object file: No such file or
directory
library libanaperfusion.so.3.2 successfully loaded.
libanasurfmatch.so.3.2.1: libanasurfmatch.so.3.2.1: cannot open shared object file: No such file or
directory
library libanasurfmatch.so.3.2 successfully loaded.
libanaroibase.so.3.2.1: libanaroibase.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libanaroibase.so.3.2 successfully loaded.
libanaroialgo.so.3.2.1: libanaroialgo.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libanaroialgo.so.3.2 successfully loaded.
libpyanatomistmodule.so.3.2.1: libpyanatomistmodule.so.3.2.1: cannot open shared object file: No su
ch file or directory
PyAnatomist Module present
library libpyanatomistmodule.so.3.2 successfully loaded.
libanavolrender.so.3.2.1: libanavolrender.so.3.2.1: cannot open shared object file: No such file or
directory
library libanavolrender.so.3.2 successfully loaded.
libanavtk.so.3.2.1: libanavtk.so.3.2.1: cannot open shared object file: No such file or directory
library libanavtk.so.3.2 successfully loaded.
libsigraphsvm.so.3.2.1: libsigraphsvm.so.3.2.1: cannot open shared object file: No such file or dir
ectory
library libsigraphsvm.so.3.2 successfully loaded.
global modules: /opt/brainvisa/share/anatomist-3.2/python_plugins
home modules: /home/meg2/.anatomist/python_plugins
loading module anacontrolmenu
loading module selection
<H1>Anatomist launched</H1>
loading module volumepalettes
loading module histogram
loading module palettecontrols
loading module modelGraphs
loading module foldsplit
loading module gradientpalette
loading module meshsplit
loading module paletteViewer
all python modules loaded
-Sylvain.
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riviere
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Re: Brainvisa T1 pipeline problem
Hi Sylvain,
Well, actually in the debug messages things are OK: the plugin mechanism looks first for the most precise libraries versions (3.2.1), doesn't find them, then loads a less precise library version (3.2) and actually finds them, which is normal in brainvisa 3.2.x and 4.0.x (it will change in 4.1), and that's why these messages are confusing...
So the plugins are not loaded when anatomist is run from brainVisa. It is probably a PATH issue then. Does it happen only when brainvisa is run remotely from a windows machine, or any time brainvisa is run on the linux machine, even locally ?
Could you please post the "starting BrainVisa" section of BrainVisa log ?
Oh, and could you check, in BV preferences, in the "Anatomist" tab, that the anatomist executable is just "anatomist", or if there is a different (and so, probably wrong) value there ?
Denis
Well, actually in the debug messages things are OK: the plugin mechanism looks first for the most precise libraries versions (3.2.1), doesn't find them, then loads a less precise library version (3.2) and actually finds them, which is normal in brainvisa 3.2.x and 4.0.x (it will change in 4.1), and that's why these messages are confusing...
So the plugins are not loaded when anatomist is run from brainVisa. It is probably a PATH issue then. Does it happen only when brainvisa is run remotely from a windows machine, or any time brainvisa is run on the linux machine, even locally ?
Could you please post the "starting BrainVisa" section of BrainVisa log ?
Oh, and could you check, in BV preferences, in the "Anatomist" tab, that the anatomist executable is just "anatomist", or if there is a different (and so, probably wrong) value there ?
Denis
Re: Brainvisa T1 pipeline problem
Alright!
Here is the contents of the brainvisa log : starting brainvisa. Note I cannot run BV locally on the linux server:: it's literally a black box that I can access to only remotely. I can also send you the log from one session that works just fine, from another client machine, if you think that would be usefeul.
thanks again!
BrainVISA 3.2
Python version
2.5.1 (r251:54863, Oct 1 2008, 11:53:20) [GCC 4.0.2 20051125 (Red Hat 4.0.2-8)]
Command line
"/opt/brainvisa/bin/brainvisa"
Environment variables
SSH_ASKPASS = /usr/libexec/openssh/gnome-ssh-askpass
GROUP = neuro
REMOTEHOST = megana1.fmlh.edu
LESSOPEN = |/usr/bin/lesspipe.sh %s
HOSTTYPE = x86_64-linux
MNI_DIR = /opt/freesurfer/mni
SSH_CLIENT = 172.20.180.37 51799 22
CVS_RSH = ssh
LOGNAME = meg2
USER = meg2
INPUTRC = /etc/inputrc
HOME = /home/meg2
PATH = /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/mni/bin:/opt/brainvisa/bin/commands-links:/opt/brainvisa/bin:/opt/MNE-2.7.0-3089-Linux-x86_64/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/NX/bin:/home/meg2/bin:/usr/NX/bin
LANGUAGE = en
LD_LIBRARY_PATH = /opt/brainvisa/lib:/opt/MNE-2.7.0-3089-Linux-x86_64/lib:/opt/matlab/sys/os/glnxa64:/opt/MNE-2.7.0-3089-Linux-x86_64/lib
XUSERFILESEARCHPATH = /opt/MNE-2.7.0-3089-Linux-x86_64/share/app-defaults/%N
LANG = en_US.UTF-8
TERM = dtterm
SHELL = /bin/bash
FMRI_ANALYSIS_DIR = /opt/freesurfer/fsfast
DCMDICTPATH = /opt/brainvisa/lib/dicom.dic
SHLVL = 3
MNE_ROOT = /opt/MNE-2.7.0-3089-Linux-x86_64
NXDIR = /usr/NX
G_BROKEN_FILENAMES = 1
BRAINVISA_SYSTEM_VARIABLES = PATH DCMDICTPATH BRAINVISA_SHARE PYTHONHOME PYTHONPATH LD_LIBRARY_PATH
HISTSIZE = 1000
FREESURFER_HOME = /opt/freesurfer
MNE_LIB_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/lib
_ = /opt/brainvisa/bin/commands-links/python
MNI_PERL5LIB = /opt/freesurfer/mni/lib/perl5/5.8.0
MATLAB_ROOT = /opt/matlab
VENDOR = unknown
MINC_BIN_DIR = /opt/freesurfer/mni/bin
FSFAST_HOME = /opt/freesurfer/fsfast
PYTHONPATH = /opt/brainvisa/python:/opt/brainvisa/lib/python2.5/site-packages:
MNE_BIN_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/bin
BRAINVISA_SHARE = /opt/brainvisa/share
OSTYPE = linux
HOST = megneto
MINC_LIB_DIR = /opt/freesurfer/mni/lib
BRAINVISA_SYSTEM_LD_LIBRARY_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/lib:/opt/matlab/sys/os/glnxa64:/opt/MNE-2.7.0-3089-Linux-x86_64/lib
PERL5LIB = /opt/freesurfer/mni/lib/perl5/5.8.0
MACHTYPE = x86_64
DISPLAY = localhost:10.0
FSF_OUTPUT_FORMAT = nii
SSH_CONNECTION = 172.20.180.37 51799 192.227.56.111 22
SSH_TTY = /dev/pts/15
HOSTNAME = megneto
BRAINVISA_SYSTEM_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/NX/bin
PYTHONHOME = /opt/brainvisa/
FIX_VERTEX_AREA =
MNI_DATAPATH = /opt/freesurfer/mni/data
PWD = /home/meg2
SUBJECTS_DIR = /opt/freesurfer/subjects
LOCAL_DIR = /opt/freesurfer/local
MAIL = /var/spool/mail/meg2
LS_COLORS = no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35:
OS = Linux
FUNCTIONALS_DIR = /opt/freesurfer/sessions
FS_OVERRIDE = 0
BrainVISA options
platform = linux
gui = True
sessionID = a8d90d56-1308-dc16-95e3-996e408e2cdd
userProfile = None
siteOptionFile = /opt/brainvisa/brainvisa/options.minf
userOptionFile = /home/meg2/.brainvisa/options.minf
logFileName = /home/meg2/.brainvisa/brainvisa2.log
temporaryDirectory = /tmp
mainPath = /opt/brainvisa/brainvisa
iconPath = /opt/brainvisa/share/brainvisa-3.2/icons
typesPath = ['/opt/brainvisa/brainvisa/types', '/opt/brainvisa/brainvisa/toolboxes/brainrat/types', '/opt/brainvisa/brainvisa/toolboxes/connectomist/types', '/opt/brainvisa/brainvisa/toolboxes/cortical_surface/types', '/opt/brainvisa/brainvisa/toolboxes/morphometry/types', '/opt/brainvisa/brainvisa/toolboxes/structural_analysis/types', '/opt/brainvisa/brainvisa/toolboxes/sulci/types', '/opt/brainvisa/brainvisa/toolboxes/t1mri/types']
dataPath = [<brainvisa.configuration.databases_configuration.DatabaseSettings object at 0x9d9d2cc>, <brainvisa.configuration.databases_configuration.DatabaseSettings object at 0x9da354c>]
processesPath = ['/opt/brainvisa/brainvisa/processes']
fileSystemOntologiesPath = ['/opt/brainvisa/brainvisa/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/connectomist/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/cortical_surface/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/structural_analysis/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/sulci/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/t1mri/hierarchies']
mainDocPath = /opt/brainvisa/share/doc/brainvisa-3.2
docPath = /opt/brainvisa/share/doc/brainvisa-3.2/en
anatomistExecutable = anatomist
matlabRelease = None
matlabExecutable = matlab
matlabOptions = -nosplash -nojvm
matlabPath = ['/opt/brainvisa/brainvisa/matlab', '/opt/brainvisa/brainvisa/matlab/mesh', '/opt/brainvisa/brainvisa/matlab/utils', '/opt/brainvisa/brainvisa/matlab/LoadSave']
matlabStartup = []
spmDirectory =
logFileName = /home/meg2/.brainvisa/brainvisa2.log
language = en
userLevel = 2
startup = ["execfile('/opt/brainvisa/brainvisa/startup.py',globals(),{})"]
supportEmail = support@brainvisa.info
SMTP_server_name = localhost
flatHierarchy = /opt/brainvisa/brainvisa/shfjFlatHierarchy.py
textEditor = emacs
Here is the contents of the brainvisa log : starting brainvisa. Note I cannot run BV locally on the linux server:: it's literally a black box that I can access to only remotely. I can also send you the log from one session that works just fine, from another client machine, if you think that would be usefeul.
thanks again!
BrainVISA 3.2
Python version
2.5.1 (r251:54863, Oct 1 2008, 11:53:20) [GCC 4.0.2 20051125 (Red Hat 4.0.2-8)]
Command line
"/opt/brainvisa/bin/brainvisa"
Environment variables
SSH_ASKPASS = /usr/libexec/openssh/gnome-ssh-askpass
GROUP = neuro
REMOTEHOST = megana1.fmlh.edu
LESSOPEN = |/usr/bin/lesspipe.sh %s
HOSTTYPE = x86_64-linux
MNI_DIR = /opt/freesurfer/mni
SSH_CLIENT = 172.20.180.37 51799 22
CVS_RSH = ssh
LOGNAME = meg2
USER = meg2
INPUTRC = /etc/inputrc
HOME = /home/meg2
PATH = /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/mni/bin:/opt/brainvisa/bin/commands-links:/opt/brainvisa/bin:/opt/MNE-2.7.0-3089-Linux-x86_64/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/NX/bin:/home/meg2/bin:/usr/NX/bin
LANGUAGE = en
LD_LIBRARY_PATH = /opt/brainvisa/lib:/opt/MNE-2.7.0-3089-Linux-x86_64/lib:/opt/matlab/sys/os/glnxa64:/opt/MNE-2.7.0-3089-Linux-x86_64/lib
XUSERFILESEARCHPATH = /opt/MNE-2.7.0-3089-Linux-x86_64/share/app-defaults/%N
LANG = en_US.UTF-8
TERM = dtterm
SHELL = /bin/bash
FMRI_ANALYSIS_DIR = /opt/freesurfer/fsfast
DCMDICTPATH = /opt/brainvisa/lib/dicom.dic
SHLVL = 3
MNE_ROOT = /opt/MNE-2.7.0-3089-Linux-x86_64
NXDIR = /usr/NX
G_BROKEN_FILENAMES = 1
BRAINVISA_SYSTEM_VARIABLES = PATH DCMDICTPATH BRAINVISA_SHARE PYTHONHOME PYTHONPATH LD_LIBRARY_PATH
HISTSIZE = 1000
FREESURFER_HOME = /opt/freesurfer
MNE_LIB_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/lib
_ = /opt/brainvisa/bin/commands-links/python
MNI_PERL5LIB = /opt/freesurfer/mni/lib/perl5/5.8.0
MATLAB_ROOT = /opt/matlab
VENDOR = unknown
MINC_BIN_DIR = /opt/freesurfer/mni/bin
FSFAST_HOME = /opt/freesurfer/fsfast
PYTHONPATH = /opt/brainvisa/python:/opt/brainvisa/lib/python2.5/site-packages:
MNE_BIN_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/bin
BRAINVISA_SHARE = /opt/brainvisa/share
OSTYPE = linux
HOST = megneto
MINC_LIB_DIR = /opt/freesurfer/mni/lib
BRAINVISA_SYSTEM_LD_LIBRARY_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/lib:/opt/matlab/sys/os/glnxa64:/opt/MNE-2.7.0-3089-Linux-x86_64/lib
PERL5LIB = /opt/freesurfer/mni/lib/perl5/5.8.0
MACHTYPE = x86_64
DISPLAY = localhost:10.0
FSF_OUTPUT_FORMAT = nii
SSH_CONNECTION = 172.20.180.37 51799 192.227.56.111 22
SSH_TTY = /dev/pts/15
HOSTNAME = megneto
BRAINVISA_SYSTEM_PATH = /opt/MNE-2.7.0-3089-Linux-x86_64/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/NX/bin
PYTHONHOME = /opt/brainvisa/
FIX_VERTEX_AREA =
MNI_DATAPATH = /opt/freesurfer/mni/data
PWD = /home/meg2
SUBJECTS_DIR = /opt/freesurfer/subjects
LOCAL_DIR = /opt/freesurfer/local
MAIL = /var/spool/mail/meg2
LS_COLORS = no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35:
OS = Linux
FUNCTIONALS_DIR = /opt/freesurfer/sessions
FS_OVERRIDE = 0
BrainVISA options
platform = linux
gui = True
sessionID = a8d90d56-1308-dc16-95e3-996e408e2cdd
userProfile = None
siteOptionFile = /opt/brainvisa/brainvisa/options.minf
userOptionFile = /home/meg2/.brainvisa/options.minf
logFileName = /home/meg2/.brainvisa/brainvisa2.log
temporaryDirectory = /tmp
mainPath = /opt/brainvisa/brainvisa
iconPath = /opt/brainvisa/share/brainvisa-3.2/icons
typesPath = ['/opt/brainvisa/brainvisa/types', '/opt/brainvisa/brainvisa/toolboxes/brainrat/types', '/opt/brainvisa/brainvisa/toolboxes/connectomist/types', '/opt/brainvisa/brainvisa/toolboxes/cortical_surface/types', '/opt/brainvisa/brainvisa/toolboxes/morphometry/types', '/opt/brainvisa/brainvisa/toolboxes/structural_analysis/types', '/opt/brainvisa/brainvisa/toolboxes/sulci/types', '/opt/brainvisa/brainvisa/toolboxes/t1mri/types']
dataPath = [<brainvisa.configuration.databases_configuration.DatabaseSettings object at 0x9d9d2cc>, <brainvisa.configuration.databases_configuration.DatabaseSettings object at 0x9da354c>]
processesPath = ['/opt/brainvisa/brainvisa/processes']
fileSystemOntologiesPath = ['/opt/brainvisa/brainvisa/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/connectomist/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/cortical_surface/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/structural_analysis/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/sulci/hierarchies', '/opt/brainvisa/brainvisa/toolboxes/t1mri/hierarchies']
mainDocPath = /opt/brainvisa/share/doc/brainvisa-3.2
docPath = /opt/brainvisa/share/doc/brainvisa-3.2/en
anatomistExecutable = anatomist
matlabRelease = None
matlabExecutable = matlab
matlabOptions = -nosplash -nojvm
matlabPath = ['/opt/brainvisa/brainvisa/matlab', '/opt/brainvisa/brainvisa/matlab/mesh', '/opt/brainvisa/brainvisa/matlab/utils', '/opt/brainvisa/brainvisa/matlab/LoadSave']
matlabStartup = []
spmDirectory =
logFileName = /home/meg2/.brainvisa/brainvisa2.log
language = en
userLevel = 2
startup = ["execfile('/opt/brainvisa/brainvisa/startup.py',globals(),{})"]
supportEmail = support@brainvisa.info
SMTP_server_name = localhost
flatHierarchy = /opt/brainvisa/brainvisa/shfjFlatHierarchy.py
textEditor = emacs
-Sylvain.
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: Brainvisa T1 pipeline problem
Well, I don't see anything wrong in this log...
We can still try to get other information...
Once anatomist is run from BrainVisa, could you please open in Anatomist the info window (in the main window, the "help -> Anatomist/AIMS information" menu, and copy/paste its contents ?
Another test:
run the following commandline:(use copy/paste to avoid quote or space mistakes). It should start brainvisa and anatomist. Then go to brainvisa log, and the "Anatomist" section. Could you copy/paste the contents of this section please ?
Denis
We can still try to get other information...
Once anatomist is run from BrainVisa, could you please open in Anatomist the info window (in the main window, the "help -> Anatomist/AIMS information" menu, and copy/paste its contents ?
Another test:
run the following commandline:
Code: Select all
brainvisa -c 'from brainvisa import anatomist; a=anatomist.Anatomist( "--debugLevel", "2" )'Denis
Re: Brainvisa T1 pipeline problem
Here is the contents of the anatomist info window:
Data type: object/object - formats : PYTHON XML
- Graph sub-formats readers:
Generic
CorticalFoldArg
model_graph
roi
- AIMS settings:
{
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 1,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 1,
'spm_output_4d_volumes' : 1,
'nifti_output_4d_volumes' : 1,
'default_writers' : {
'Mesh' : 'MESH',
'Volume' : 'NIFTI1'
}
}
Data type: object/object - formats : PYTHON XML
- Graph sub-formats readers:
Generic
CorticalFoldArg
model_graph
roi
- AIMS settings:
{
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 1,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 1,
'spm_output_4d_volumes' : 1,
'nifti_output_4d_volumes' : 1,
'default_writers' : {
'Mesh' : 'MESH',
'Volume' : 'NIFTI1'
}
}
-Sylvain.
Re: Brainvisa T1 pipeline problem
and the contents of the brainvisa/anatomist log section when using the command line with debugLevel 2
Starting Anatomist.....
libaimsvida.so.3.2.1: libaimsvida.so.3.2.1: cannot open shared object file: No such file or directory
libaimsdicom.so.3.2.1: libaimsdicom.so.3.2.1: cannot open shared object file: No such file or directory
libaimsecat.so.3.2.1: libaimsecat.so.3.2.1: cannot open shared object file: No such file or directory
libaimsfdf.so.3.2.1: libaimsfdf.so.3.2.1: cannot open shared object file: No such file or directory
libaimsjpeg.so.3.2.1: libaimsjpeg.so.3.2.1: cannot open shared object file: No such file or directory
libaimstiff.so.3.2.1: libaimstiff.so.3.2.1: cannot open shared object file: No such file or directory
libaimsqtformats.so.3.2.1: libaimsqtformats.so.3.2.1: cannot open shared object file: No such file or directory
libaimsminc.so.3.2.1: libaimsminc.so.3.2.1: cannot open shared object file: No such file or directory
libaimsply.so.3.2.1: libaimsply.so.3.2.1: cannot open shared object file: No such file or directory
libaimsnifti.so.3.2.1: libaimsnifti.so.3.2.1: cannot open shared object file: No such file or directory
libaimsgifti.so.3.2.1: libaimsgifti.so.3.2.1: cannot open shared object file: No such file or directory
libconnectomist_aims_plugin.so.3.2.1: libconnectomist_aims_plugin.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsvida.so.3.2 successfully loaded.
library libaimsdicom.so.3.2 successfully loaded.
library libaimsecat.so.3.2 successfully loaded.
library libaimsfdf.so.3.2 successfully loaded.
library libaimsjpeg.so.3.2 successfully loaded.
library libaimstiff.so.3.2 successfully loaded.
library libaimsqtformats.so.3.2 successfully loaded.
library libaimsminc.so.3.2 successfully loaded.
library libaimsply.so.3.2 successfully loaded.
library libaimsnifti.so.3.2 successfully loaded.
library libaimsgifti.so.3.2 successfully loaded.
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
config file : /home/meg2/.anatomist/config/settings.cfg
libanafold.so.3.2.1: libanafold.so.3.2.1: cannot open shared object file: No such file or directory
libanahistogram.so.3.2.1: libanahistogram.so.3.2.1: cannot open shared object file: No such file or directory
libanaprofile.so.3.2.1: libanaprofile.so.3.2.1: cannot open shared object file: No such file or directory
libanaperfusion.so.3.2.1: libanaperfusion.so.3.2.1: cannot open shared object file: No such file or directory
libanasurfmatch.so.3.2.1: libanasurfmatch.so.3.2.1: cannot open shared object file: No such file or directory
libanaroibase.so.3.2.1: libanaroibase.so.3.2.1: cannot open shared object file: No such file or directory
libanaroialgo.so.3.2.1: libanaroialgo.so.3.2.1: cannot open shared object file: No such file or directory
libpyanatomistmodule.so.3.2.1: libpyanatomistmodule.so.3.2.1: cannot open shared object file: No such file or directory
libanavolrender.so.3.2.1: libanavolrender.so.3.2.1: cannot open shared object file: No such file or directory
libanavtk.so.3.2.1: libanavtk.so.3.2.1: cannot open shared object file: No such file or directory
libsigraphsvm.so.3.2.1: libsigraphsvm.so.3.2.1: cannot open shared object file: No such file or directory
library libanafold.so.3.2 successfully loaded.
library libanahistogram.so.3.2 successfully loaded.
library libanaprofile.so.3.2 successfully loaded.
library libanaperfusion.so.3.2 successfully loaded.
library libanasurfmatch.so.3.2 successfully loaded.
library libanaroibase.so.3.2 successfully loaded.
library libanaroialgo.so.3.2 successfully loaded.
PyAnatomist Module present
library libpyanatomistmodule.so.3.2 successfully loaded.
library libanavolrender.so.3.2 successfully loaded.
library libanavtk.so.3.2 successfully loaded.
library libsigraphsvm.so.3.2 successfully loaded.
Server on port 50007, now listening
global modules: /opt/brainvisa/share/anatomist-3.2/python_plugins
home modules: /home/meg2/.anatomist/python_plugins
loading module anacontrolmenu
loading module selection
<H1>Anatomist launched</H1>
loading module volumepalettes
loading module histogram
loading module palettecontrols
loading module modelGraphs
loading module foldsplit
loading module gradientpalette
loading module meshsplit
loading module paletteViewer
all python modules loaded
new connection
Starting Anatomist.....
libaimsvida.so.3.2.1: libaimsvida.so.3.2.1: cannot open shared object file: No such file or directory
libaimsdicom.so.3.2.1: libaimsdicom.so.3.2.1: cannot open shared object file: No such file or directory
libaimsecat.so.3.2.1: libaimsecat.so.3.2.1: cannot open shared object file: No such file or directory
libaimsfdf.so.3.2.1: libaimsfdf.so.3.2.1: cannot open shared object file: No such file or directory
libaimsjpeg.so.3.2.1: libaimsjpeg.so.3.2.1: cannot open shared object file: No such file or directory
libaimstiff.so.3.2.1: libaimstiff.so.3.2.1: cannot open shared object file: No such file or directory
libaimsqtformats.so.3.2.1: libaimsqtformats.so.3.2.1: cannot open shared object file: No such file or directory
libaimsminc.so.3.2.1: libaimsminc.so.3.2.1: cannot open shared object file: No such file or directory
libaimsply.so.3.2.1: libaimsply.so.3.2.1: cannot open shared object file: No such file or directory
libaimsnifti.so.3.2.1: libaimsnifti.so.3.2.1: cannot open shared object file: No such file or directory
libaimsgifti.so.3.2.1: libaimsgifti.so.3.2.1: cannot open shared object file: No such file or directory
libconnectomist_aims_plugin.so.3.2.1: libconnectomist_aims_plugin.so.3.2.1: cannot open shared object file: No such file or directory
library libaimsvida.so.3.2 successfully loaded.
library libaimsdicom.so.3.2 successfully loaded.
library libaimsecat.so.3.2 successfully loaded.
library libaimsfdf.so.3.2 successfully loaded.
library libaimsjpeg.so.3.2 successfully loaded.
library libaimstiff.so.3.2 successfully loaded.
library libaimsqtformats.so.3.2 successfully loaded.
library libaimsminc.so.3.2 successfully loaded.
library libaimsply.so.3.2 successfully loaded.
library libaimsnifti.so.3.2 successfully loaded.
library libaimsgifti.so.3.2 successfully loaded.
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
config file : /home/meg2/.anatomist/config/settings.cfg
libanafold.so.3.2.1: libanafold.so.3.2.1: cannot open shared object file: No such file or directory
libanahistogram.so.3.2.1: libanahistogram.so.3.2.1: cannot open shared object file: No such file or directory
libanaprofile.so.3.2.1: libanaprofile.so.3.2.1: cannot open shared object file: No such file or directory
libanaperfusion.so.3.2.1: libanaperfusion.so.3.2.1: cannot open shared object file: No such file or directory
libanasurfmatch.so.3.2.1: libanasurfmatch.so.3.2.1: cannot open shared object file: No such file or directory
libanaroibase.so.3.2.1: libanaroibase.so.3.2.1: cannot open shared object file: No such file or directory
libanaroialgo.so.3.2.1: libanaroialgo.so.3.2.1: cannot open shared object file: No such file or directory
libpyanatomistmodule.so.3.2.1: libpyanatomistmodule.so.3.2.1: cannot open shared object file: No such file or directory
libanavolrender.so.3.2.1: libanavolrender.so.3.2.1: cannot open shared object file: No such file or directory
libanavtk.so.3.2.1: libanavtk.so.3.2.1: cannot open shared object file: No such file or directory
libsigraphsvm.so.3.2.1: libsigraphsvm.so.3.2.1: cannot open shared object file: No such file or directory
library libanafold.so.3.2 successfully loaded.
library libanahistogram.so.3.2 successfully loaded.
library libanaprofile.so.3.2 successfully loaded.
library libanaperfusion.so.3.2 successfully loaded.
library libanasurfmatch.so.3.2 successfully loaded.
library libanaroibase.so.3.2 successfully loaded.
library libanaroialgo.so.3.2 successfully loaded.
PyAnatomist Module present
library libpyanatomistmodule.so.3.2 successfully loaded.
library libanavolrender.so.3.2 successfully loaded.
library libanavtk.so.3.2 successfully loaded.
library libsigraphsvm.so.3.2 successfully loaded.
Server on port 50007, now listening
global modules: /opt/brainvisa/share/anatomist-3.2/python_plugins
home modules: /home/meg2/.anatomist/python_plugins
loading module anacontrolmenu
loading module selection
<H1>Anatomist launched</H1>
loading module volumepalettes
loading module histogram
loading module palettecontrols
loading module modelGraphs
loading module foldsplit
loading module gradientpalette
loading module meshsplit
loading module paletteViewer
all python modules loaded
new connection
-Sylvain.