Do you also use SCT and would like to share your feedback with the community? Please add your testimonial by clicking here. Thank you 😊
Christian Büchel, MD | Universitätsklinikum Hamburg-Eppendorf | Hamburg 🇩🇪
SCT is an invaluable tool for our investigations of central pain processing in the spinal cord using fMRI. In addition, our combined cortico-spinal imaging approach greatly benefits from the accurate spatial prepossessing capabilities of SCT.
Douglas Arnold, MD | NeuroRx & McGill University | Montreal 🇨🇦
Easily implemented. Beautiful output of state-of-the-art results.
Claudia Gandini Wheeler-Kingshott, PhD | NMR Research Unit, UCL | London 🇬🇧
We use SCT for all our spinal cord analysis in studies of Multiple Sclerosis as well as Spinal Cord Injury and ataxia. I also used SCT in the first study of SC involvement in dementia.
Robert Barry, PhD | Harvard/MGH Martinos Center | Boston 🇺🇸
The Spinal Cord Toolbox is an excellent (free and open-source) resource for anybody interested in conducting spinal cord research. I am currently using it for multiple projects, and plan to continue using it in the future. The community forum has been particularly helpful because my questions have been addressed in a timely fashion - and have resulted in quick bug fixes and additional features. Funding agencies interested in supporting collaborative and reproducible research may view the Spinal Cord Toolbox as a worthwhile investment.
Yazhuo Kong, PhD | Institute of Psychology, Chinese Academy of Sciences | Beijing 🇨🇳
I have been working on spinal cord MRI for some years and I cannot make it without the help of SCT. The segmentation, co-registration and MNI template etc are great features in the SCT toolbox, fast and reliable. We have published papers in high impact journals such as PNAS and Brain, using SCT as the main analysis tool. SCT is well documented and the forum is really helpful as well. We can always get very quick replies for any questions there! So huge thanks to the SCT team for their hard work and contribution to spinal cord imaging research.
Kenneth Weber, PhD | Stanford University | Palo Alto 🇺🇸
Our team uses SCT for processing of structural and functional spinal cord MRI datasets. Our goal is to develop quantitative markers of pain and sensorimotor function, which we hope will improve our ability to diagnose and treat conditions afflicting the central nervous system. We have 18 publications that have used SCT and more than 10 projects that are in progress. The SCT community quickly responds to any questions and issues (typically within a day), and I find the SCT documentation and community forum to be very helpful and detailed. Ultimately, our research would not be possible without SCT, particularly the normalization tools. SCT will be seen as turning point in quantitative spinal cord MRI. I have already seen rapid growth in the field since the SCT release.
Joo-won Kim, PhD | Baylor College of Medicine | Houston 🇺🇸
SCT is a powerful tool to process and analyze spinal cord MRI with minimal manual procedures. It’s been actively developed and maintained.
Kouhei Kamiya, MD, PhD | Toho University | Tokyo 🇯🇵
I use SCT basically for segmentation and quantitative measurement of spinal cord MRI for my research, including some on-going works. SCT is well documented, and instruction at the website as well as the workshop helped me a lot. The best thing I like about SCT is that it is user-friendly and the results are easy to use for publication in papers.
Jonathan Brooks, PhD | University of East Anglia | Norwich 🇬🇧
Honestly, as one of the original developers of spinal functional imaging, I think this field would not have thrived as much as it has without the developments that Julien and his co-workers have given the community. They have applied cutting edge techniques and robust validation pipelines to ensure that researchers can (hopefully) say sensible things about their data. In particular, the spatial normalisation of spinal imaging data across individuals is a major achievement, without which we’d still be floundering in the dark. The team have put on a variety of free seminars (and webinars) across the globe to help users get up to speed, and are always incredibly responsive when contacted via online forums. Not much else to say other than “Bravo!”.
Falk Eippert, PhD | Max Planck Institute for Human Cognitive and Brain Sciences | Leipzig 🇩🇪
SCT is of invaluable help in the processing of spinal fMRI data - with its arrival the sometimes annoying combination of routines from SPM, FSL and ANTS that I used beforehand is now a thing of the past. The probabilistic maps that are included (e.g. tissue type or segmental level) also help a lot with respect to establishing a standardized and meaningful way of reporting results across the community. I’m especially grateful for how quickly the SCT team responds to issues that come up and how they implement user requests regarding new features. And finally, it’s really impressive how SCT has grown (since its first release in 2014) in terms of the functionality it offers as well as its documentation (command-specific help, online forum, workshops).
Marco Loggia, PhD | MGH, Harvard Med School | Boston 🇺🇸
Over the last few years, our lab has been using SCT mostly to perform spinal cord PET imaging. This tool has enabled us to perform, automatically and very easily, image analyses that would be otherwise extremely laborious. Even more impressive is how responsive Julien and his team are. We love this tool!
David Cadotte, MD, PhD | University of Calgary | Calgary 🇨🇦
At the University of Calgary we are using SCT to process both routine clinical MRI scans (commonly used to confirm a diagnosis of degenerative cervical myelopathy) and advanced imaging protocols of diffusion imaging, magnetization transfer imaging and t2* acquisitions of the human spinal cord in states of both ‘health’ and disease. We are incorporating the derived metrics into prediction algorithms to help patients understand their spinal cord condition and make informed decisions about treatment options. The SCT is very well documented but the community forum and development team are an incredible asset to aid in the successful implementation of the tools available within the SCT. Congratulations to Professor Cohen-Adad and his incredible team for making this project a success that is resonating with patients across the country!
Francesco Grussu, PhD | Vall d’Hebron Institute of Oncology | Barcelona 🇪🇸
I have been a user of SCT since its first release. My work has so far focused on advanced spinal cord MRI (mainly diffusion MRI), and when I approached this field there were no well-established tools to process spinal cord MRI data yet (2012). However, since its first release back in 2015ish-2016ish, SCT has really changed how we work in spinal cord MRI: the toolbox has equipped MRI physicists and radiologists with an interest in spinal cord with a powerful set of tools to deal with all standard (yet, extremely important) preprocessing. I have published 2 papers as a first author using SCT, and I have co-authored more. I cannot think of working on spinal cord MRI without relying on such a well-documented toolbox - which, least but not last, works extremely well, and is managed by a fantastic team who replies within minutes to any question one may have. To conclude, the SCT is a fantastic tool for the spinal cord MRI community, and as a spinal cord MRI scientist I am really thankful to the team for having made my life so much easier.
Haykel Snoussi, PhD | Data and Imaging Analyst, UT Health San Antonio, Texas | 🇺🇸
I used SCT during my PhD for the process of Diffusion MRI data of spinal cord in the context of multiple sclerosis disease. Using this toolbox, I was able to publish two conference papers.
Marios Yiannakas, PhD | University College London (UCL) | London 🇬🇧
SCT facilitates research into spinal cord imaging in no other known reliable, respected, and cost-free alternative currently available. Genuinely grateful for the effort behind this, and the vision altogether, super thankful, and fully supportive of the maintenance of it, without a doubt.
Satoshi Maki MD, PhD | Chiba University | Chiba 🇯🇵
SCT made a breakthrough enabling the quantification of spinal cord MRI in a modern way. It also has a helpful community forum even for newbies.
Maria Marcella Lagana, PhD | IRCCS Fondazione Don Carlo Gnocchi ONLUS | Milan 🇮🇹
I use SCT for quantifying the spinal cord cross-sectional area and the spinal cord diffusion properties in a study of subjects with Multiple Sclerosis. The SCT documents, courses, and recordings have been very useful for learning how to use the software and for knowing its updates. The interactions with the forum are prompt and useful for any doubts. The past SCT workshops have also been useful to write consensus guidelines about quantitative spinal cord MRI acquisition and processing.
Ben Davies MD, MPhil | University of Cambridge | Cambridge 🇬🇧
Degenerative Cervical Myelopathy - Clinical Research. New to the platform, but ongoing study exploring its value as a radiological endpoints for the disease. I attended one of the SCT courses in London. I think fundamentally this is an incredible resource, easy to use even for a clinician with limited prior experience, and is enabling access to quantitative MRI of the spinal cord, which is incredibly under utilised in a wide range of diseases. The team, led by JCA are incredibly supportive, able to answer emails and share the science which underpins and drives the platform forward.
Karina Robles, BSc | National Autonomous University of Mexico | Mexico City 🇲🇽
I’m using SCT for fMRI of patients who had a Cerebrovascular Event. I’ve never posted on the forum, but other questions have helped me to understand the questions I have. I like SCT because it is a friendly toolbox for processing cervical image data.
Maxime Descoteaux, PhD | Université de Sherbrooke | Sherbrooke 🇨🇦
User-friendly, clear documentation, large community, rapid release, can be trusted. I love it and you guys should be proud of the tool. It is also used in my company Imeka Solutions Inc as well as others out there. (response above is 5/5 best)
Marcello Moccia, MD, PhD | University of Naples | Naples 🇮🇹
SCT has sped up our spinal cord research in multiple sclerosis. We are now processing spinal cord images from clinical trials and practice.
Sergio Daniel Hernandez Charpak, MSc | EPFL | Lausanne 🇨🇭
I am using SCT in a fMRI context. I have used it in different steps, as segmentation of the CSF and spinal cord in the lumbar region, or to perform motion correction. This has been a challenge and we are at the border of the technically feasible. SCT has been crucial in making it possible. The documentation and the community forum are world class. Every time I have used them (the forum, the git, or simply the documentation), I have been amazed by the response time and quality of the responses. It is definitively an example of an open source project bringing scientists together to push the boundaries of knowledge.
Patrick Freund, MD, PhD | University of Zurich | Zurich 🇨🇭
We use the SCT for tissue-specific segmentation and preprocessing of spinal cord fRMI data.
Emil Ljungberg, PhD | King’s College London | London 🇬🇧
I was an early adopter of the spinal cord toolbox and started using it in 2015 for doing basic segmentation of the spinal cord. It later became instrumental in my MSc project for quantitative myelin water imaging. What makes SCT really great is the community, including an active online forum and workshops around ISMRM. The SCT team also publish great articles about the techniques which are essential references when using the tools in publications.
Rosella Tro’, PhD | University of Genoa | Genova 🇮🇹
My experience with SCT concerns computation of Diffusion Kurtosis Imaging measures on neonatal subjects in the spinal cord district. Specifically, through the constant support of SCT community members, I was able to implement an analysis pipeline from image acquisition to computation of metrics through registration with atlas. All steps were adapted for neonatal age range from the default adult ones. This pipeline has then been applied to a pilot case study. I really appreciate this open-source, user-friendly software as well as availability of its creators for any question or issue.
Jon Stutters, BEng | UCL | London 🇬🇧
We use SCT for investigations into spinal cord injury and multiple sclerosis. Analysis using SCT has contributed to several MS clinical trials in which we are involved. I find SCT to be well documented and each of its tools has a clear purpose. I also appreciate that it is made available under an open license.
Romina Mariano, MD, PhD | University of Oxford | Oxford 🇬🇧
My research focus is spinal cord involvement in neuro-inflammatory conditions of the central nervous system. SCT is an invaluable resource for spinal cord imaging. SCT is well documented but additionally the workshops and online community forum are useful for added support. My research has also shown that SCT is useful for clinical research with potential for direct clinical applicability in the future. The spinal cord is under-studied due to the difficulty experienced in cord imaging and analysis but with tools such as SCT we will make great strides in our understanding of important neurological conditions and symptoms that will have a significant impact for academia but also for the quality of life of our patients.
Mohammed Khamaysa, MD, PhD student | Sorbonne university, INSERM | Paris 🇫🇷
I am using SCT for treating MRIs at spinal levels in ALS patients; including structural images and DTI to obtain quantitative metrics. I have been using SCT for 2 years, and I have found it easy to use with minimal knowledge on imaging processing. It would be helpful to have more example data with the ways to analyze them. Thank you so much for providing this powerful tool.
Alicia Cronin | Robarts Research Institute | London 🇨🇦
Currently, we use SCT to segment the spinal cords of Degenerative Cervical Myelopathy patients. We have used SCT in our study to quantify spinal cord compression in these patients. When first starting with SCT, I attended the Spinal Cord Workshop, which was very helpful for setting up the program and the basic functions. Any other problems I have encountered have been well documented in the posted tutorials and forum online. It is very easy to use and there is plenty of help online.
Nawal Kinany, PhD | University of Geneva | Geneva 🇨🇭
Great toolbox that I have, so far, mostly used to process spinal cord fMRI data. The SCT offers powerful tools to bring this field forward and to enable more uniform & robust analyses (segmentation, normalization to a common template, etc.). The toolbox is well documented, with useful workshops and a very responsive team. Thanks for that!
Ibrahim Hattan, MD, PhD | University of Queensland | 🇦🇺
I’m using SCT to analyze ex vivo human spinal cord data. There are a huge progress in my analysis using the amazing features in term of segmentation, registration, etc. The SCT is well documented and there are much work from its team by recorded courses (available publicly) for users from all over the world. Personally, I’ve received valuable assistance and useful feedback from the SCT community. Also, the SCT team helped me to generate a specific deep learning model and implemented it in SCT software (to benefit other users) in order to segment our ex-vivo tissues. I’m extremely grateful to all of the SCT community for their help, support, effort and wish this community the best in their future work and development.
Mahdi Alizadeh, PhD | Thomas Jefferson University | Philadelphia 🇺🇸
I used SCT for diffusion processing of the spinal cord. Software itself was well documented for me.
Shiva Shahrampour, MSc | Thomas Jefferson University | Philadelphia 🇺🇸
My major line of work is pediatric spinal cord imaging analysis. I have been using SCT as the major tool for my analysis and have been very satisfied with the result. The toolbox provides comprehensive and robust tools for the spinal cord segmentation of multimodal images, spinal cord registration, atlas based analysis of white matter tracts and many other useful applications. SCT has saved me from going back and forth between several applications while working on our dataset. The community forum is absolutely helpful and responsive when there’s an issue with the dataset or analysis. They do take the time to make sure they address the questions in a timely manner. Bottom line, I am glad SCT exists and I highly recommend it. Kudos to SCT dev team!
Merve Kaptan, MSc | Max Planck Institute for Human Cognitive and Brain Sciences | Leipzig 🇩🇪
As a PhD student who did not work with spinal cord fMRI data before, I found SCT very very helpful. It is very nice to have a dedicated toolbox with functions tailored to spinal cord acquisitions. Currently, I am working on a project in which we used the automated segmentation functionality of the SCT to automate a procedure and this was very helpful! Also Dr. Cohen-Adad and other SCT experts are very helpful and quick to reply if one encounters problems. I cannot recommend it enough. :)
Abdullah Althobity, MD, PhD candidate | Ministry of Education | Riyadh 🇸🇦
I used SCT to segment lumbar spinal cord regions of EAE mouse model for multiple sclerosis. The model has been trained very well by Charley and Julien after I sent them some samples. They helped me from installing the software to the final step. Then all my data, which is over 70 mice, have been easy to analyse without any error. The biggest advantage of SCT that I or any colleague can run any segmentation in a consistent way. The forum is very useful where I get all answers for any question in a very quick way.
Arash Forodighasemabadi, MSc | Aix-Marseille University | 🇫🇷
I use SCT on a daily basis, since my project is related to the microtrauma of cervical spinal cord. I am satisfied with SCT and its documentation and help. I rarely visit the community forum, since I have not yet encountered big problems and errors (that I cannot find solutions to in the help).