[slicer-users] Fwd: Python Stochastic Tractography Module - trying to duplicate tutorial results

Andrew Rausch rauscha at bwh.harvard.edu
Fri Mar 26 16:25:29 EDT 2010


Forwarding my response to slicer-users.

---------- Forwarded message ----------
From: Andrew Rausch <rauscha at bwh.harvard.edu>
Date: Wed, Mar 24, 2010 at 4:39 PM
Subject: Re: [slicer-users] Python Stochastic Tractography Module - trying
to duplicate tutorial results

Hi,
I've got a few suggestions, but I'll be happy to take more questions as I
can answer them.
Looking at the slicer stochastic issues, my first question is which nightly
version you are using, but I doubt that's the issue.

1) It's fine to not see vtkMRML ScalarVolumeNode3 - the Baseline image that
you're interested in is Diffusion Tensor Estimation Volume1, as you selected
while running Diffusion Tensor Estimation by clicking "Create New Volume"

2) having Bg give a word after the number suggests to me that you have
loaded whichever image you have in the background as a label map, while you
should have the baseline loaded as a greyscale image...

3) Are you sure you have selected the "Enable Slicer Demon" checkbox?

4) I don't know the deep specifics of the stochastic code, so i can't look
and see what's causing these errors, but it looks like you may not be giving
it a good DWI image. Are you maybe plugging in an extracted tensor image
instead or something like that?

-Andrew


On Tue, Mar 23, 2010 at 3:49 PM, Andrew Rausch <rauscha at bwh.harvard.edu>wrote:

> Hi all,
> Sorry for the delayed response, I've been away from the lab. I'm looking at
> this right now on linux and having no problems, I'll move to a windows
> computer and see if I can replicate it there.
> -Andrew
>
>
>
> On Thu, Mar 18, 2010 at 6:22 PM, Marek Kubicki <kubicki2 at verizon.net>wrote:
>
>> Right now I forward all the questions to Adrew, who knows stochastic
>> tractography module the best, Ryan is still learning.
>> Marek
>>
>>
>>
>> On Mar 18, 2010, at 3:53 PM, Steve Pieper wrote:
>>
>>  This question just came on the slicer-users list - a timely follow-on to
>>> Ron's question - who can answer questions on this topic?
>>>
>>>
>>> -------- Original Message --------
>>> Subject:        [slicer-users] Python Stochastic Tractography Module -
>>> trying
>>> to duplicate tutorial results
>>> Date:   Thu, 18 Mar 2010 14:32:21 -0500
>>> From:   Mark Alexiuk <malexiuk at imris.com>
>>> To:     <slicer-users at bwh.harvard.edu>
>>>
>>>
>>>
>>> Hi – I’m working through a tutorial and am having some trouble
>>> duplicating the results. Details follow. Thanks in advance for your help
>>> and suggestions.
>>>
>>> Cheers
>>>
>>> Mark
>>>
>>> The Tutorial:
>>>
>>> Slicer3 Training Tutorial - Python Stochastic Tractography Module
>>>
>>> http://www.na-mic.org/Wiki/images/b/be/Stochastic_June09_1.ppt
>>>
>>> The slicer3 version specifically mentioned in the tutorial:
>>>
>>> Slicer 3 Software (Slicer 3.5 nightly build as of January 3rd, 2010)
>>>
>>> My slicer3 version:
>>>
>>> 3D Slicer Version 3.5 Alpha 1.0 (3D Slicer Version 3.5 Alpha1.0)
>>> [Windows XP Pro, SP3]
>>>
>>> Problem steps?:
>>>
>>> On slide 18 “thresholding baseline” is the volume name
>>> vtkMRMLScalarVolumeNode3 generated automatically, I don’t see it listed
>>> in the dropdown box.
>>>
>>> On slide 19 “baseline intensities” I should see Bg<value>. I see instead
>>> “Bg-14 components”.
>>>
>>> On slide 33 there is a command window with output from the python
>>> script. I never see this – a command window opens and closes rapidly.
>>>
>>> Warnings and errors:
>>>
>>> Warning: In ..\..\VTK\Filtering\vtkDataSetAttributes.cxx, line 1040
>>>
>>> vtkPointData (0F91BCA0): Can not set attribute Tensors. Incorrect number
>>> of components.
>>>
>>> ERROR: In ..\..\..\Slicer3\Libs\vtkTeem\vtkDiffusionTensorGlyph.cxx,
>>> line 228
>>>
>>> vtkDiffusionTensorGlyph (0F937408): No data to glyph!
>>>
>>> <Attached Message Part.txt>
>>>
>>
>>
>
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