[slicer-users] Problem using Resample Scalar/Vector/DWI

Steve Pieper pieper at bwh.harvard.edu
Tue Nov 23 07:58:47 EST 2010


Hmm, I don't see anything obviously wrong with it, but the next place to 
look I think is MRMLIDImageIO::SetDWNodeValues at line 726 of 
Libs/MRMLIDImageIO/itkMRMLIDImageIO.cxx.  This is where the dwi 
gradients get converted from ITK to MRML when running as a shared 
library module.

Anybody see an issue there?

-Steve

On 11/22/2010 04:49 PM, Francois Budin wrote:
> Steve and Jim, the file that is suppose the write the file out is
> ResampleVolume2.cxx (Slicer3/Applications/CLI). It is updating the
> writer line 1205.
> I am modifying the MetaDataDictionary around line 981.
> Demian, I see the bug you are talking about but it has been corrected
> and it is slightly different this time. Last time there was a problem
> of dividing the norm by 0 if I remember correctly. This time this case
> is handled properly, but for some reason, when starting the module in
> Slicer as a shared module, something is not written back properly in
> Slicer at the end.
>
> Francois
>
> On Mon, Nov 22, 2010 at 4:23 PM, Demian Wassermann
> <demian at bwh.harvard.edu>  wrote:
>> Hi All,
>>
>> I had reported this error at some point. It came from the fact that ResampleDTI was dividing the gradient directions by its norm at some point in order to reorient the direction of the gradients. Maybe some new fix brought the bug back.
>>
>> Cheers
>> Demian
>>
>> --
>> Demian Wassermann, PhD
>> demian at bwh.harvard.edu
>> LMI / PNL / SPL Labs
>> Harvard Medical School
>> Brigham and Women's Hospital
>> 1249 Boylston, Boston, MA, USA
>>
>> On Nov 22, 2010, at 6:18 PM, Steve Pieper wrote:
>>
>>> Hi Francois -
>>>
>>> I'm cc'ing Jim Miller on this - he may have an idea why passing the DWI
>>> data to/from a shared library module is different than going via a
>>> command line.
>>>
>>> One possibility, it seems to me, is that the pointer might be on the
>>> stack and it could be go out of scope before it gets loaded back to the
>>> scene - can you send the info on the file and line number where you set
>>> the data and where the writer is invoked?
>>>
>>> -Steve
>>>
>>> On 11/22/2010 01:56 PM, Francois Budin wrote:
>>>> Hi everyone,
>>>>
>>>> The problem only appears when the module is loaded in Slicer as a
>>>> shared object. If the module is compiled only as an executable file,
>>>> then the output is correct, even when used directly in Slicer. I am
>>>> not sure if it is a problem with Slicer or with my module.
>>>>
>>>> Francois
>>>>
>>>> On Fri, Nov 19, 2010 at 4:37 PM, Francois Budin<budin at bwh.harvard.edu>    wrote:
>>>>> I really have no idea where the problem is coming from. I tried to
>>>>> print out the values that are saved as NaN and they are 0,0,0 while
>>>>> the module is running. If somebody has any idea that would be very
>>>>> helpful.
>>>>>
>>>>> Francois
>>>>>
>>>>> On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel<stan.oubel at gmail.com>    wrote:
>>>>>> Hi Dominik,
>>>>>>
>>>>>> Good idea! Thanks!
>>>>>>
>>>>>> stan
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>>>>>>
>>>>>>> Hi Stan,
>>>>>>>
>>>>>>> Francois is correct, I think. I've encountered a similar issue
>>>>>>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>>>>>>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>>>>>>> module and the diffusion editor and manually enter 0 where you see an NaN.
>>>>>>> That worked for me.
>>>>>>>
>>>>>>> Dominik
>>>>>>>
>>>>>>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> I tried to find where the problem was from and here is what I found:
>>>>>>>> -If I run the module outside of Slicer it works
>>>>>>>> -If I do it inside Slicer, I get the following error:
>>>>>>>> ERROR: In
>>>>>>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>>> line 1575
>>>>>>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>>>>>>> terminated with a fault.
>>>>>>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>>>>>>> [NaN NaN NaN]. I am trying to figure out why.
>>>>>>>>
>>>>>>>> Francois
>>>>>>>>
>>>>>>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<stan.oubel at gmail.com>
>>>>>>>>   wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>>>>>>> an
>>>>>>>>> option
>>>>>>>>> to create specific DW volumes.
>>>>>>>>>
>>>>>>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>>>>>>> sequence I get another error:
>>>>>>>>>
>>>>>>>>> ERROR: In
>>>>>>>>>
>>>>>>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>>>> line 1575
>>>>>>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>>>>>>> terminated with an unknown exception.
>>>>>>>>>
>>>>>>>>> However, I don't have this error when computing the tensor of the
>>>>>>>>> original
>>>>>>>>> DWI sequence. Any ideas?
>>>>>>>>>
>>>>>>>>> Thanks!
>>>>>>>>>
>>>>>>>>> stan
>>>>>>>>>
>>>>>>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hi Estanislao,
>>>>>>>>>>
>>>>>>>>>> What did you select as the output volume? Did you select "Create New
>>>>>>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>>>>>>> Sincerely,
>>>>>>>>>>
>>>>>>>>>> Francois
>>>>>>>>>>
>>>>>>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>>>>>>> Oubel<stan.oubel at gmail.com>
>>>>>>>>>>   wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Hi all,
>>>>>>>>>>>
>>>>>>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>>>>>>> Scalar/Vector/DWI volume
>>>>>>>>>>> What I do is the following:
>>>>>>>>>>>
>>>>>>>>>>> 1. I load the dwi sequence
>>>>>>>>>>> 2. Create a transform node from the Data menu
>>>>>>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>>>>>>> Transform
>>>>>>>>>>> Node in the module.
>>>>>>>>>>>
>>>>>>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>>>>>>> the
>>>>>>>>>>> following error in the error
>>>>>>>>>>> log window:
>>>>>>>>>>>
>>>>>>>>>>> ERROR: In
>>>>>>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>>>>>>> line 278
>>>>>>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>>>>>>> NumberOfScalarComponents,
>>>>>>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>>>>>>
>>>>>>>>>>> What I'm doing wrong?
>>>>>>>>>>>
>>>>>>>>>>> thanks!
>>>>>>>>>>>
>>>>>>>>>>> stan
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>
>>>>>>
>>>>>>
>>>>>
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