[slicer-users] Fwd: Python Stochastic Tractography Module - trying to duplicate tutorial results
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
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?
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.
> 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.
>> 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 -
>>> 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.
>>> The Tutorial:
>>> Slicer3 Training Tutorial - Python Stochastic Tractography Module
>>> 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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