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Analyzed 11 days ago. based on code collected about 2 months ago.
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 ... [More] 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 [Less]
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?
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 ... [More] 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 [Less]
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
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
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 ... [More] 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 [Less]
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: ... [More] 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. [Less]
Posted almost 10 years ago by Julien Cohen-Adad
The presentation of the SCToolbox hands-on workshop can be downloaded here.
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
Posted almost 10 years ago by Julien Cohen-Adad
http://sourceforge.net/projects/spinalcordtoolbox/files/2.0/patch_2.0.3.zip/download