help{basic questions}

pestoo · Post by **pestoo** » Thu Oct 11, 2007 3:49 am

I'm a new person who just knew brainvisa. I have read the handbook but I still don't know how to start. Because I saw many kinds of formats of the figures needed but I don't have them.

Please don't laugh at me.

I have just some MRI.img, and I want to get the brain surface (3D) and then get some sulcus labeled, can you tell me what should I do?

Thank you very much.!!

Post by **Dominique Geffroy** » Thu Oct 11, 2007 9:30 am

Hello,

You can use your image in Brainvisa, .img are recognized.

You have first to import your image in Brainvisa using process "data management/import/anatomy/import T1 MRI". You must have choosen before a directory as database (to store data) in menu Preferences/Databases.

Then you can use the anatomical pipeline to compute several meshes and graphs from your image :
- Run "anatomy/t1 pipeline 2004/Prepare subject for anatomical pipeline" to place acpc coordinates in your image
- then you can run "anatomy/t1 pipeline 2004/ana do a lot of things from t1 mri" (this is the pipeline)

To label sulci, use "anatomy/morphometry/automatic recognition" process.

You will find documentation in brainvisa about these processes.

pestoo · Post by **pestoo** » Thu Oct 11, 2007 12:09 pm

Thanks for your reply. I have a problem when I proceed.....

When I use "Ana do a lot of things" of my subject, the program would stop for these information. I don't think it's the memory problem because I have enough space. Then how can I fix the problem?

Thank you very much!!

s Ana Do A Lot of Things from T1 MRI 2 started on 2007/10/11 19:02
------------------------------
! VIP Warning:
Something was wrong with the iterative erosion!
------------------------------

------------------------------
!! VIP Error:
Not enough memory...
------------------------------
Error while allocating Vip3DPoint_S16BIT vector
------------------------------
!! VIP Error:

Execution aborted in function '(Vip_alloc.c)VipMalloc'.

------------------------------

------------------------------
!! VIP Error:

Execution aborted in function 'VipMalloc3DBucket_S16BIT'.

------------------------------

------------------------------
! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------

------------------------------
! VIP Warning:
Nothing is left in VipConnexVolumeFilter
------------------------------
Can't allocate memory - no memory left.
St9bad_alloc
Can't allocate memory - no memory left.

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.

in Vip Split Brain 3 RuntimeError: System command exited with non null value : 3

neuroProcesses.py (1641) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (107) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (932) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (1721) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

in Ana Split Brain from Brain Mask 3 RuntimeError: System command exited with non null value : 3

neuroProcesses.py (1641) in _processExecution:
result = process.execution( self )
AnaSplitBrainFromBrainMask.py (69) in execution:
Commissure_coordinates = self.Commissure_coordinates )
neuroProcesses.py (1534) in runProcess:
result = self._processExecution( _process )
neuroProcesses.py (1641) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (107) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (932) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (1721) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

alexis · Post by **alexis** » Thu Oct 11, 2007 3:14 pm

Dear pestoo,

I also don't think that it's a memory problem ( but we could be more precise if you gave us you cpu speed and ram ). This could be linked to a bad configuration. So here are some questions :

- In "Ana do a lot of things", what has been put in the "Comissure_coordinates" field ?
- When you performed the "Prepare Subject" process, what were the resulting coordinates ?

Alexis

pestoo · Post by **pestoo** » Fri Oct 12, 2007 3:39 am

Hello Alexis,

Thank you.

My computer : Intel(R) Core(TM)2 CPU
6300 @1.86GHZ
1.86GHZ,0.99GB of RAM

Here my subject name is :sub107.ima

__In "Ana do a lot of things",in the "Comissure_ coordinates" field, it's "sub107.APC".(I didn't input it, but when I chose subject in "T1 MRI", the .APC appeared in the field automatically.)

__In" prepare", Anterior_Commissure: 128.5 115.5 115.0
Posterior_Commissure: 129.5 134.5 125.0
Interhemispheric_Point:126.5 105.5 71.0

This is the result of running the "prepare"program:

voxel size: [1, 1, 1, 1]
IH plane normal: [-0.88013094793721613, -0.4735487165531761, 0.033483242584568008]
image is axial
front is on the expected side
upside on the top. OK

Thanks for your reply~!!!!

Post by **Dominique Geffroy** » Fri Oct 12, 2007 1:05 pm

I don't see where can be the problem. Maybe you can send me your image by email, so we can try and say if the problem comes from the data or the configuration...

pestoo · Post by **pestoo** » Fri Oct 12, 2007 1:39 pm

Hello,

Thanks!!

I have sent you my image.

By the way, I have tried another image, this times it works better than the first one but there are still some warnings like the previous one. When I checked the meshes produced, they are ugly and don't have sulci~~ Is it because the coordinates were not well chosen??

Thank you for help@!!!

pestoo · Post by **pestoo** » Sat Oct 13, 2007 11:13 am

Hello,

Now I want to state another problem that i faced.
I tried another two images, this time it didn't stop without any results. But there are some warnings I think which are the reasons that cause my results ugly.

------------------------------
! VIP Warning:
Risky regularization, gray matter to close to 0, skip!
------------------------------

------------------------------
! VIP Warning:
Something was wrong with the iterative erosion!
------------------------------

------------------------------
! VIP Warning:
Empty volume in VipGet3DConnex

-----------------------------
! VIP Warning:
Nothing is left in VipConnexVolumeFilter

In the end when I checked my data, the .mesh files don't have details about gyrus and sulci, and no data about the whole head.

Could you tell me that what is the problem with my program?

Thank you so much.

Post by **riviere** » Sat Oct 13, 2007 1:22 pm

Hi,

All those problems may happen when early processing steps fail for any reason. Such reasons may include low quality images, inadequate resolutions (our pipelines work best at about 1mm voxel resolution), inexpected bias field or contrast...
The first thing is: check image resolution
Then restart the pipeline after changing the bias type and/or contrast type. If it stil doesn't work, then it may be the image quality which would be a problem...

Denis

pestoo · Post by **pestoo** » Wed Oct 31, 2007 2:54 pm

Hi,
thank you. I've tried the ways you said. Neither works. sigh.

By the way, how to check image resolution? I don't know the method,can you tell me ? Many thanks.

There is another question, I have the 3D surfaces of the brains in fact, but the format is .byu, which can not be recognized by the software. Can I change it to the format which can be recognized by the software/>??

I think if I can convert the format directly, there would be no need to deal with the MRI images, it is really an tiring work with no improvement.

Plz help . Thanks.!

riviere wrote:Hi,

All those problems may happen when early processing steps fail for any reason. Such reasons may include low quality images, inadequate resolutions (our pipelines work best at about 1mm voxel resolution), inexpected bias field or contrast...
The first thing is: check image resolution
Then restart the pipeline after changing the bias type and/or contrast type. If it stil doesn't work, then it may be the image quality which would be a problem...

Denis

Post by **riviere** » Fri Nov 02, 2007 12:31 am

Well, if it doesn't work with the standards settings, then it may be necessary to go to lower-level parameters tuning.
The image resolution is just the voxel sizes, you can check it using AimsFileConvert, or using anatomist, or also using brainvisa, the voxel_size property is amongst the attributes shown on a selected image in the database search dialog box (the red magnifying glass icon).

But if you only need to retreive the existing mesh, you are right, there is maybe no need to process it with brainvisa.
However the mesh format conversion is still perhaps a problem. Our tools don't know the .byu format. The supported mesh formats is quite restricted, and our own formats are not known to the rest of the world. But you can try to convert it to VRML1 or to .pov (pov ray format) which are.. at least partly supported...
Otherwise you would need to write a format conversion program yourself... The description of our .mesh format is on the web site, it is a very simple format.

Denis

pestoo · Post by **pestoo** » Thu Nov 29, 2007 7:11 am

Thanks a lot.
I tried to find the resolution of the image:

file_type = GIS
voxel_size = [1, 1, 1, 1]
volume_dimension = [256, 256, 256, 1]
data_type = S16
object_type = Volume

So do you think that my image is not so bad?
By the way, i have tried to convert my .byu to .pov, then I want to label the sulci of the brain. So I choose "anatomy/morphometry/automatic recognition" process. But the problem is that ....POV is not .arg or .mesh, it looks like that the software can not recognize it. Is it true or I have done something wrong?

Thanks for telling me!

riviere wrote:Well, if it doesn't work with the standards settings, then it may be necessary to go to lower-level parameters tuning.
The image resolution is just the voxel sizes, you can check it using AimsFileConvert, or using anatomist, or also using brainvisa, the voxel_size property is amongst the attributes shown on a selected image in the database search dialog box (the red magnifying glass icon).

But if you only need to retreive the existing mesh, you are right, there is maybe no need to process it with brainvisa.
However the mesh format conversion is still perhaps a problem. Our tools don't know the .byu format. The supported mesh formats is quite restricted, and our own formats are not known to the rest of the world. But you can try to convert it to VRML1 or to .pov (pov ray format) which are.. at least partly supported...
Otherwise you would need to write a format conversion program yourself... The description of our .mesh format is on the web site, it is a very simple format.

Denis

Post by **riviere** » Thu Nov 29, 2007 1:59 pm

Hi,

For the anatomical pipeline problem, then it may be necessary to tune some processing parameters. Without seing the image, I cannot help you, and I'm afraid I don't have much time to process it for you...
Have you tried other images ?

For the sulci labeling, the sulci recognition process does not take a mesh as input, so there is no way your .pov might work. The input fot this process is a structural representation of the cortical folds, a graph (.arg), which is produced by the segmentation pipeline (when it works). So if you cannot make the segmentation tools to work, forget about the sulci labeling...

Denis