Dear Brainvisa expert,
I use the Fedora core 1. When I do "Ana Do A Lot of things in T1", it always hang on AimsGraphConvert" step without any error message. I wait for 2 hours but the program did not go further step. I only get left side but no right side skeleton or roots. This conditon occurs in latest stable version (2.3.5) of brainvisa and development version. How to do ? thanks for your help.
sincerely
hang on AimsGraphConvert ? how to do ?
hang on AimsGraphConvert ? how to do ?
JLH
neurologist
neurologist
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Hi,
Well... I don't know... Have you tried to process the same data on another machine or another system ? Just to determine if the hang problem is specific to Fedora Core 1 or not... We experienced such hangs on this system but we have found and included a workaround, so it should be something else here.
Can you send us a logfile from BrainVisa (use the support menu) ?
Denis
Well... I don't know... Have you tried to process the same data on another machine or another system ? Just to determine if the hang problem is specific to Fedora Core 1 or not... We experienced such hangs on this system but we have found and included a workaround, so it should be something else here.
Can you send us a logfile from BrainVisa (use the support menu) ?
Denis
3 questions and need help how to do ?
Dear Brainvisa expert,
thanks for replay and I find the problems ike this.
1. I use the Fedora core 1, when I install stable version of brainvisa (2.3.5), I can NOT aunch the anatomist. it is blank window and the error message like this:
Starting Anatomist.....
55 palettes loaded
config file : /home/bic/khs001/.anatomist/config/settings.cfg
Syntax /data/noel/noel3/hosung/SHFJ_pack-stable-linux-2.3.5/share/anatomist/syntax/anatomist_attributes.stx read
Syntax /data/noel/noel3/hosung/SHFJ_pack-stable-linux-2.3.5/share/anatomist/syntax/graph.stx read
........
Segmentation fault
But when I use the development version, the anatomist CAN work fine. how to do ?
2. In development version. I find the final step before freeze is AimsGraphConvert. the error message is like:
can not find the file:
/home/JL//home/JL/MRI/Lgraph_new.data can not find the file.
It is very strange, I type the /home/JL/MRI/Lgraph_new.arg in the box region when I execute the Ana Do A Lot of Thing in T1 MR. Did I set the wrong name for Lgraph/Rgraph ? why it always repeat /home/JL/ before what I type ?
3. In development version, when I try to use "Ana Do A Lot of Thing in T1 MR", all the list boxe are blank, rather than in stable version (2.3.5), which it can automatic fill the correct name on the boxes when I choice the mri file ? how to do ?
thanks for replay
tulu
thanks for replay and I find the problems ike this.
1. I use the Fedora core 1, when I install stable version of brainvisa (2.3.5), I can NOT aunch the anatomist. it is blank window and the error message like this:
Starting Anatomist.....
55 palettes loaded
config file : /home/bic/khs001/.anatomist/config/settings.cfg
Syntax /data/noel/noel3/hosung/SHFJ_pack-stable-linux-2.3.5/share/anatomist/syntax/anatomist_attributes.stx read
Syntax /data/noel/noel3/hosung/SHFJ_pack-stable-linux-2.3.5/share/anatomist/syntax/graph.stx read
........
Segmentation fault
But when I use the development version, the anatomist CAN work fine. how to do ?
2. In development version. I find the final step before freeze is AimsGraphConvert. the error message is like:
can not find the file:
/home/JL//home/JL/MRI/Lgraph_new.data can not find the file.
It is very strange, I type the /home/JL/MRI/Lgraph_new.arg in the box region when I execute the Ana Do A Lot of Thing in T1 MR. Did I set the wrong name for Lgraph/Rgraph ? why it always repeat /home/JL/ before what I type ?
3. In development version, when I try to use "Ana Do A Lot of Thing in T1 MR", all the list boxe are blank, rather than in stable version (2.3.5), which it can automatic fill the correct name on the boxes when I choice the mri file ? how to do ?
thanks for replay
tulu
JLH
neurologist
neurologist
Hi,
I think that a part of yours problems is you don't use a data base BrainVISA. This data base is not always necessary but if you want use process like "Ana Do a lot of things" then it is very recommended.
To do this, here two points :
First : Set a database
Preference --> click on "Add" and select a directory (it will be your database) and then click on "Ok"
Secund : Import your data
A database is organised with 3 levels : name of proto, name of subject, and data belonging to the subject.
Import = association between a MRI T1(for instance) and a name of proto / a name of subject.
Select "Data Management -> Import -> Anatomy -> Import T1MRI"
- Set T1 MRI with the icon "browser" of "input"
- Set a proto and a subject with the icon "red magnifying glass" of "output"
- And click on Run
After this, return to "Ana Do a lot of things" process, select your T1 with "green magnifying glass" and all boxes must be filled automatically.
Isa
I think that a part of yours problems is you don't use a data base BrainVISA. This data base is not always necessary but if you want use process like "Ana Do a lot of things" then it is very recommended.
To do this, here two points :
First : Set a database
Preference --> click on "Add" and select a directory (it will be your database) and then click on "Ok"
Secund : Import your data
A database is organised with 3 levels : name of proto, name of subject, and data belonging to the subject.
Import = association between a MRI T1(for instance) and a name of proto / a name of subject.
Select "Data Management -> Import -> Anatomy -> Import T1MRI"
- Set T1 MRI with the icon "browser" of "input"
- Set a proto and a subject with the icon "red magnifying glass" of "output"
- And click on Run
After this, return to "Ana Do a lot of things" process, select your T1 with "green magnifying glass" and all boxes must be filled automatically.
Isa
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Does the stable version of anatomist crash at startup, or when you open, or use, a 3D window ?
What kind of 3D card / driver are you using ? For instance wit ATI cads, the driver has a bug that prevents anatomist from correctly working in the stable pack (2.3.5) but which has been partially worked around in the development version. Could it be the cause of the problem ?
Denis
What kind of 3D card / driver are you using ? For instance wit ATI cads, the driver has a bug that prevents anatomist from correctly working in the stable pack (2.3.5) but which has been partially worked around in the development version. Could it be the cause of the problem ?
Denis
display in anatomist problem
Dear Isa,Denis and brainvisa expert,
thanks for quick replay. I use the notebook and video card is ATI 9200M. when I click anatomist, no figure pop_out. I am not sure if it is videocard problem, but if I need to use the stable version. how can I do ?
sincerely
thanks for quick replay. I use the notebook and video card is ATI 9200M. when I click anatomist, no figure pop_out. I am not sure if it is videocard problem, but if I need to use the stable version. how can I do ?
sincerely
JLH
neurologist
neurologist
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riviere
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Problems with ATI cards appear when 3D is involved: this means anatomist starts, you will be able to see and use the control window, but it will crash when you open or use (I don't remember exactly) a 3D view. You can test it by running anatomist alone (without brainvisa). If it crashes directly at startup, then it's something else.
I think I remember problems can be avoided by disabling 3D accelaration with ATI cards. Another option is to install and use drivers made by ATI, but in our experience they were buggy too (but we haven't tested the latest ones) and quite difficult to install.
I don't remember exactly how to disable 3D acceleration...
The last solution is to replace your 3D card by a Nvidia card and drivers from nvidia (we don't want to make any advertisement but their drivers are good enough for us and it's the only 3D config that we can be sure of).
Denis
I think I remember problems can be avoided by disabling 3D accelaration with ATI cards. Another option is to install and use drivers made by ATI, but in our experience they were buggy too (but we haven't tested the latest ones) and quite difficult to install.
I don't remember exactly how to disable 3D acceleration...
The last solution is to replace your 3D card by a Nvidia card and drivers from nvidia (we don't want to make any advertisement but their drivers are good enough for us and it's the only 3D config that we can be sure of).
Denis