Spinal Cord Toolbox

Dear SCT users, We are happy to announce a new SCT release! https://github.com/neuropoly/spinalcordtoolbox/releases/tag/v4.0.0-beta.0 This is a beta version for now, until we gather your feedback and fix a few remaining issues. Changes to release: ... [More] https://github.com/neuropoly/spinalcordtoolbox/blob/release/CHANGES.md Installation instruction: https://github.com/neuropoly/spinalcordtoolbox/blob/master/README.md#installation If you have any question or feature request, please post on the forum: https://sourceforge.net/p/spinalcordtoolbox/discussion/help/ Happy processing! The Spinal Cord Toolbox Team [Less]

Dear SCT users, We are happy to announce a new SCT release! https://github.com/neuropoly/spinalcordtoolbox/releases/tag/v3.2.7 Changes to release: https://github.com/neuropoly/spinalcordtoolbox/blob/release/CHANGES.md Installation instruction: ... [More] https://github.com/neuropoly/spinalcordtoolbox/blob/master/README.md#installation If you have any question or feature request, please post on the forum: https://sourceforge.net/p/spinalcordtoolbox/discussion/help/ Happy processing! The Spinal Cord Toolbox Team [Less]

Hi, Did this course already happened this year? Best regards, Carolina Machado

Dear SCT users, We are happy to announce a new release of the Spinal Cord Toolbox! The new 3.1.1 release can be downloaded here: https://github.com/neuropoly/spinalcordtoolbox/releases Changes to release: ... [More] https://github.com/neuropoly/spinalcordtoolbox/blob/release/CHANGES.md This release introduces two new segmentation methods based on convolutional neural networks (deep-learning): - sct_deepseg_sc: automatic segmentation of the spinal cord - sct_deepseg_gm: automatic segmentation of the gray matter (more information: arxiv.org/abs/1710.01269) Installation instruction: 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 am running sct_propseg and I would like to know why the segmentation stops growing, which stop condition has been met. I could not find any log files and I tried -v 1 to get more output, but did not find this information. Any suggestions would be greatly appreciated. Thanks! Iman Brouwer

Hi SCT Team, I'm running to an issue trying to create inverse warping field for dmri data. I want to register all my subjects' dmri data to template to run between group analysis. I know that I can use -initwarp and -initwarpinv with ... [More] sct_register_multimodal command for registering Anat to template. However, I am having a little problem trying to register the dmri data to template, since I use a warp field created through registration of template to my medic (t2star) image for initwarp in my dmri registration. It's my command: sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d dwi_moco_mean.nii.gz -dseg dwi_moco_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,smooth=0,iter=3,gradStep=1 -initwarp ../medic/warp_template2medic_reg_gm.nii.gz -owarp warp_template2dmri.nii.gz How can I add the -initwarpinv option to it? Or, is there any other way that I can register my dmri data to template? Thanks a lot in advance! Haleh [Less]

Hi, We organize courses on SCT, each year, after the ISMRM conference. If you'd like to be added to the mailing list, please send an email to [email protected]. N.B.: Courses are free! Best, Julien

Dear SCT users, The new 3.1 release is out and can be downloaded here: https://github.com/neuropoly/spinalcordtoolbox/releases Changes to release: https://github.com/neuropoly/spinalcordtoolbox/blob/release/CHANGES.md Installation instruction: ... [More] 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]

First public release: June 14th 2014 https://github.com/neuropoly/spinalcordtoolbox/commit/075eaf7870b1c3f7206eca44c95f4ce9e60e0a43