tractor-mri.org.uk

TractoR ~ Home

From your MR scanner to Analyze/NIfTI format. Apply image processing operations of many types to medical image data. Perform linear and nonlinear image registration. Preprocess diffusion MR data and calculate tensor metrics including fractional anisotropy (FA), mean diffusivity (MD), and principal directions (see diffusion processing. Run probabilistic tractography using single seed points or one or more masks. Remove false positive tracts using a model of tract shape variability. With contributions and ...

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TractoR ~ Home | tractor-mri.org.uk Reviews

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From your MR scanner to Analyze/NIfTI format. Apply image processing operations of many types to medical image data. Perform linear and nonlinear image registration. Preprocess diffusion MR data and calculate tensor metrics including fractional anisotropy (FA), mean diffusivity (MD), and principal directions (see diffusion processing. Run probabilistic tractography using single seed points or one or more masks. Remove false positive tracts using a model of tract shape variability. With contributions and ...

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3 changelog

4 references

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6 convert dicom files

7 and hnt tutorial

8 site contents

9 the getting started

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TractoR ~ Home | tractor-mri.org.uk Reviews

https://tractor-mri.org.uk

From your MR scanner to Analyze/NIfTI format. Apply image processing operations of many types to medical image data. Perform linear and nonlinear image registration. Preprocess diffusion MR data and calculate tensor metrics including fractional anisotropy (FA), mean diffusivity (MD), and principal directions (see diffusion processing. Run probabilistic tractography using single seed points or one or more masks. Remove false positive tracts using a model of tract shape variability. With contributions and ...

INTERNAL PAGES

tractor-mri.org.uk

1

TractoR: Magnetic Resonance Imaging and Tractography with R

http://www.tractor-mri.org.uk/paper/index.html

TractoR: Magnetic Resonance Imaging and Tractography with R. Jonathan D. Clayden, Susana Muñoz Maniega, Amos J. Storkey, Martin D. King, Mark E. Bastin and Chris A. Clark. Please note that this is an updated version of the original TractoR paper. Which was published in the. Journal of Statistical Software. In 2011. Please cite the reference below if you use TractoR in your work. Journal of Statistical Software 44. For more information about the package and its authors. Magnetic resonance imaging (MRI) is...

2

TractoR ~ TractoR and DICOM

http://www.tractor-mri.org.uk/TractoR-and-DICOM

TractoR provides some facilities for working with DICOM files, but the DICOM standard. Please remember that TractoR is provided with no warranty. It is always advisable to check that your files are being correctly interpreted, for example with regard to orientation, before using these facilities on a regular basis. TractoR script allows you to list all of the DICOM tags in a particular file, along with their values. For example,. Tractor dicomtags $TRACTOR HOME/tests/data/dicom/01.dcm. Starting TractoR e...

3

TractoR ~ Conventions

http://www.tractor-mri.org.uk/conventions

This page discusses certain conventions specific to TractoR. TractoR is designed to work with MRI data sets, each consisting of a series of magnetic resonance images, potentially including structural, diffusion-weighted and functional images. The package stores all images and other files within a managed file hierarchy called a session. The overall layout of a session directory is shown below. Session.top-level session directory /tractor.main managed directory /transforms.stored transformatio...But if th...

4

TractoR ~ Home

http://www.tractor-mri.org.uk/home

From your MR scanner to Analyze/NIfTI format. Apply image processing operations of many types to medical image data. Perform linear and nonlinear image registration. Preprocess diffusion MR data and calculate tensor metrics including fractional anisotropy (FA), mean diffusivity (MD), and principal directions (see diffusion processing. Run probabilistic tractography using single seed points or one or more masks. Remove false positive tracts using a model of tract shape variability. With contributions and ...

5

TractoR ~ HNT tutorial

http://www.tractor-mri.org.uk/HNT-tutorial

This tutorial describes how to use TractoR to perform neighbourhood tractography using the heuristic method described in Ref. (1). Heuristic neighbourhood tractography (HNT) uses a reference tract as a guide to the topology of the white matter structure that needs to be segmented. The alternative probabilistic approach. Details of the underlying methods can be found there. TractoR experiment scripts that may be used in a typical HNT-based study are. The prerequisites for HNT are some fully preprocessed.

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flakery.org

TractoR on Windows: Experience with the Subsystem for Linux

https://www.flakery.org/tractor-on-windows-experience-with-the-subsystem-for-linux

TractoR on Windows: Experience with the Subsystem for Linux. The medical image analysis platform for which I am the main developer and maintainer, is built on the multiplatform R language. But much of its additional infrastructure is Unix-based. That has meant that researchers using Windows have previously had to jump through some rather awkward hoops to use it. The newly-released Windows 10 Anniversary Update. Installing the Windows Subsystem for Linux (WSL) is pretty straightforward. This is when thing...

flakery.org

Splitting a git branch by files modified

https://www.flakery.org/splitting-a-git-branch-by-files-modified

Splitting a git branch by files modified. Two of the nice things about git. Are the ability to create lightweight branches, and the ability to rewrite commit history to rationalise things after the fact. As a relatively recent migrant from Subversion, however, these are things that I sometimes forget about, and I therefore don't always make full use of them. Recently, I was working away on some new developments to TractoR. First to reply was @mjdominus. Who suggested using a loop:. Can't handle merge com...

homepages.ucl.ac.uk

Jonathan D. Clayden

http://www.homepages.ucl.ac.uk/~sejjjd2

Jonathan D. Clayden. I am a Lecturer (Assistant Professor) in neuroimaging and biophysics at the Institute of Child Health. ICH) within University College London. One important tool that is available to explore connectivity is diffusion magnetic resonance imaging. Which can elucidate the patterns of “wiring” in the living brain. It is assumed that if these pathways are interrupted, the brain will become internally disconnected, with negative consequences for cognition. Additionally, f...44 (0)20 7905 2708.

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TractoR ~ Home

From your MR scanner to Analyze/NIfTI format. Apply image processing operations of many types to medical image data. Perform linear and nonlinear image registration. Preprocess diffusion MR data and calculate tensor metrics including fractional anisotropy (FA), mean diffusivity (MD), and principal directions (see diffusion processing. Run probabilistic tractography using single seed points or one or more masks. Remove false positive tracts using a model of tract shape variability. With contributions and ...

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