[Mrtrix-discussion] streamtrack error

[Jeurissen Ben]

Hi Markus,

MRtrix comes with a beautiful step by step manual on how to perform fiber tractography: http://www.brain.org.au/software/mrtrix/tractography/index.html
The 'streamtrack' command also comes with an elaborate description: http://www.brain.org.au/software/mrtrix/commands/streamtrack.html

Looking into either of these documents will reveal that:

-          'streamtrack DT_STREAM' does not take tensors as input, but DW images. If you supply the DW images as a nii file, it also requires that you specify a gradient table with the -grad argument.

-          'streamtrack SD_STREAM' does not take tensors as input (since it is not tensor based), but FOD spherical harmonic coefficients. A complete walkthrough on this is at http://www.brain.org.au/software/mrtrix/tractography/index.html.

Cheers,
Ben


From: mrtrix-discussion-bounces at public.nitrc.org [mailto:mrtrix-discussion-bounces at public.nitrc.org] On Behalf Of Markus Gschwind
Sent: zondag 13 november 2011 10:48
To: mrtrix-discussion at public.nitrc.org
Subject: [Mrtrix-discussion] streamtrack error

Dear Mrtrix specialists,

I am completely new to Mrtrix and am trying to get it to work.
When doing streamtrack commands however I seem to meet problems.

I tried both DT_STREAM and SD_STREAM, bot none of them worked.

Below please see  the error messages.

I'd like to ask what seems wrong. Is it te tensor image itself? I created it using dwi2tensor form DICOM images.

The CC_mask.nii is a binary mask (1 layer), handdrawn on the corpus callosum.

Thanks in advance!
Markus Gschwind


markus$ streamtrack -debug -info -seed CC_mask.nii DT_STREAM tensor.nii CC_tract

streamtrack [INFO]: opening image "tensor.nii"...
streamtrack [DEBUG]: preparing file "./tensor.nii"
streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)
streamtrack [DEBUG]: sanitising transformation matrix...
streamtrack [DEBUG]: unmapping file "./tensor.nii"
streamtrack [DEBUG]: setting up image "tensor.nii"...
streamtrack [DEBUG]: sanitising transformation matrix...
streamtrack [DEBUG]: setting up data increments for "tensor.nii"...
streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 704512 ]
streamtrack [INFO]: error parsing spherical ROI specification "CC_mask.nii" - assuming mask image
streamtrack [DEBUG]: mapping image "tensor.nii"...
streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)
streamtrack [DEBUG]: data mapper for image "tensor.nii" mapped with segment size = 4227072 (optimised)
streamtrack [INFO]: launching 1 threads
streamtrack [INFO]: found 0x0 diffusion-weighted encoding
streamtrack: invalid gradient matrix dimensions
streamtrack [INFO]: closing image "tensor.nii"...
streamtrack [DEBUG]: unmapping file "./tensor.nii"




Markus-Gschwinds-MacBook-Pro:Case_SSS markus$ streamtrack -debug -info -seed CC_mask.nii SD_STREAM tensor.nii CC_tract

streamtrack [INFO]: opening image "tensor.nii"...
streamtrack [DEBUG]: preparing file "./tensor.nii"
streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)
streamtrack [DEBUG]: sanitising transformation matrix...
streamtrack [DEBUG]: unmapping file "./tensor.nii"
streamtrack [DEBUG]: setting up image "tensor.nii"...
streamtrack [DEBUG]: sanitising transformation matrix...
streamtrack [DEBUG]: setting up data increments for "tensor.nii"...
streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 704512 ]
streamtrack [INFO]: error parsing spherical ROI specification "CC_mask.nii" - assuming mask image
streamtrack [DEBUG]: mapping image "tensor.nii"...
streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)
streamtrack [DEBUG]: data mapper for image "tensor.nii" mapped with segment size = 4227072 (optimised)
streamtrack [INFO]: launching 1 threads
streamtrack [INFO]: opening image "CC_mask.nii"...
streamtrack [DEBUG]: preparing file "./CC_mask.nii"
streamtrack [DEBUG]: file "./CC_mask.nii" mapped at 0x102021000, size 1409376 (read-only)
streamtrack [DEBUG]: sanitising transformation matrix...
streamtrack [DEBUG]: unmapping file "./CC_mask.nii"
streamtrack [DEBUG]: setting up image "CC_mask.nii"...
streamtrack [DEBUG]: sanitising transformation matrix...
streamtrack [DEBUG]: setting up data increments for "CC_mask.nii"...
streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 ]
streamtrack [DEBUG]: mapping image "CC_mask.nii"...
streamtrack [DEBUG]: file "./CC_mask.nii" mapped at 0x102021000, size 1409376 (read-only)
streamtrack [DEBUG]: data mapper for image "CC_mask.nii" mapped with segment size = 704512
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!
streamtrack [INFO]: failed to find SH peak!



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