Spinal Cord Toolbox

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]

Hi, I want to ask, does SCT (spinal cord tool box) prefer to register dti to the anatomical scan or the other way around?

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]

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

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

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]

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]

The presentation of the SCToolbox hands-on workshop can be downloaded here.

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

http://sourceforge.net/projects/spinalcordtoolbox/files/2.0/patch_2.0.3.zip/download