Posted
about 8 years
ago
by
Julien Cohen-Adad
Dear SCT users,
The new 3.0.0 release is out and can be downloaded here:
https://github.com/neuropoly/spinalcordtoolbox/releases
Changes to release are listed here:
https://github.com/neuropoly/spinalcordtoolbox/blob/release/CHANGES.md
Installation
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instruction are here:
https://sourceforge.net/p/spinalcordtoolbox/wiki/installation/
If you have any question or feature request, please post on the forum:
https://sourceforge.net/p/spinalcordtoolbox/discussion/help/
Best,
The Spinal Cord Toolbox Team
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Posted
over 8 years
ago
by
Sidra Khan
Hi,
I want to ask, does SCT (spinal cord tool box) prefer to register dti to the anatomical scan or the other way around?
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Posted
about 9 years
ago
by
Joan Goldsworthy
Trying to track down the problem. sct_label_vertebrae references sct_straighten_spinalcord, which references sct_concat_transfo, which is approximately where the error was generated in sct_straighten_spinalcord just by looking at the printed
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statements. Last few lines of output preceeding error as follows:
*Estimate b-spline transformation: curve --> straight...
isctANTSLandmarksBSplineTransform tmp.landmarksstraight.nii.gz tmp.landmarkscurved.nii.gz tmp.curve2straightrigid.txt tmp.warpcurve2straight.nii.gz 3x3x5 3 LandmarksRealCurve.txt LandmarksRealStraight.txt 3 0
crop
isctcropimage -i tmp.landmarksstraight.nii.gz -o tmp.landmarksstraightcrop.nii.gz -dim 0,1,2 -bmax
Cropping the following region:
Dimension 0: 159 221
Dimension 1: 159 221
Dimension 2: 29 81
Done! To view results, type:
fslview tmp.landmarksstraightcrop.nii.gz &
Concatenate rigid and non-linear transformations...
sctconcattransfo -w tmp.curve2straightrigid.txt,tmp.warpcurve2straight.nii.gz -d tmp.landmarksstraightcrop.nii.gz -o tmp.curve2straight.nii.gz
ERROR: The file tmp.curve2straightrigid.txt does not exist. Exit program.
*
sct_testing ran without errors excepting a fail on sct_get_centerline. Propseg and process_segmentation worked well, but this error is identical whether using output from propseg or process_segmentation as an input.
Any help is appreciated.
Thanks
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Posted
about 9 years
ago
by
Benjamin De Leener
Hi,
We are happy to announce a new SCT release: v2.2
It can be downloaded here:
https://sourceforge.net/projects/spinalcordtoolbox/files/2.2/
Changes are listed here:
https://github.com/neuropoly/spinalcordtoolbox/blob/master/CHANGES.md
Enjoy :-)
The Spinal Cord Toolbox Team
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Posted
over 9 years
ago
by
Julien Cohen-Adad
Hi,
We are happy to announce a new SCT release: v2.1
It can be downloaded here:
https://sourceforge.net/projects/spinalcordtoolbox/files/2.1/
Major changes are listed here:
https://github.com/neuropoly/spinalcordtoolbox/blob/master/CHANGES.md
Enjoy :-)
The Spinal Cord Toolbox Team
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Posted
over 9 years
ago
by
Julien Cohen-Adad
At the Neuroimaging Research Laboratory (www.neuro.polymtl.ca) based at Ecole Polytechnique, Université de Montréal, we work to better understand the brain and the spinal cord using state-of-the-art imaging techniques, with many potential medical
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applications. We are developing advanced analysis methods to improve the quality of MRI data, as well as to extract meaningful clinical information.
We are looking for a full-time developer/manager to contribute to an open-source software package: the Spinal Cord Toolbox http://sourceforge.net/projects/spinalcordtoolbox/
The main activities will be to:
• Manage the project
• Lead a small team of students and developers (5-10 people)
• Establish best practices for coding, testing and software releases
• Organize courses for researchers and clinicians at international conferences
The position is for one year, renewable. Salary will range from 50$k-70$k/year, commensurate with experience, and will also include competitive benefits.
Starting date: December 1st 2015 or later (up to 3 months).
What profile are we looking for?
• Strong coding skills in Python and C/C++
• Experience in project and team management
• Passion for open-source software and data science
• Long-term involvement
Why take this job?
• Join an environment that fosters autonomy, passion and creativity
• Get the opportunity to take leadership in open-source projects
• Develop strong image processing skills with experts in neuroimaging.
• Our team is committed to high-quality work, both in terms of
publications and of open-source software.
• Develop a highly multidisciplinary network of collaborators, including
computer scientists, neuroscientists and medical doctors.
How to apply?
Send to [email protected]:
• CV (include your realizations)
• Letter of motivation
• Name + email of three contact persons
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Posted
over 9 years
ago
by
Joshua Purvis
Hi all,
So I had errors when running a scan through the DTI steps, and when I ran sct_check_dependences this error came up.
Check which OS is running...
linux (Linux-3.16.0-44-generic-x86_64-with-Ubuntu-14.10-utopic)
Check RAM...
MemTotal:
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3881232 kB
total used free shared buffers cached
Mem: 3790 3571 218 400 35 826
-/+ buffers/cache: 2709 1080
Swap: 3927 1020 2907
Check which Python is running ...
/usr/bin/python
Fetch version of the Spinal Cord Toolbox...
version: 2.0.6
Check if pillow is installed .......................Traceback (most recent call last):
File "/home/taublab/spinalcordtoolbox/bin/sct_check_dependences", line 478, in
main()
File "/home/taublab/spinalcordtoolbox/bin/sct_check_dependences", line 137, in main
pillow_version = get_package_version("pillow")
File "/home/taublab/spinalcordtoolbox/bin/sct_check_dependences", line 435, in get_package_version
raise Exception("Could not find package: "+package_name)
Exception: Could not find package: pillow
I tried redownloading all of the dependences, but the error still shows.
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Posted
almost 10 years
ago
by
Julien Cohen-Adad
The presentation of the SCToolbox hands-on workshop can be downloaded here.
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Posted
almost 10 years
ago
by
Julien Cohen-Adad
Download patch:
http://sourceforge.net/projects/spinalcordtoolbox/files/2.0/patch_2.0.4.zip/download
Release notes:
https://github.com/neuropoly/spinalcordtoolbox/blob/master/CHANGES.md
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Posted
almost 10 years
ago
by
Julien Cohen-Adad
http://sourceforge.net/projects/spinalcordtoolbox/files/2.0/patch_2.0.3.zip/download
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