DTI Protocols « ENIGMA DTI Protocols « ENIGMA

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Spatial Normalization - LRCNWiki

For those that have yet to process DTI data, various suggestions are outlined here. Determine how your DWI set s are organized How many many acquisitions do you have? Therefore you will need additional software, to emulate another operating system.

Make sure T1-weighted scans and the DWI are aligned!!

You can use the output of the file from now on and to create your FA images e. We will therefore not require a specific protocol to be followed with any particular software, as long as the appropriate steps are performed. Make sure T1-weighted scans have undergone inhomogeneity NU correction.

This requires multiple steps: Directional information from the primary Eigenvector are shown. Correct for Eddy Current distortions, movement using affine registration. Correct for EPI induced susceptibility artifacts — this is particularly an issue at higher magnetic fields.

The advantage of the GUI lies in its simplicity but the drawback is the less flexibility comparing to the command-lines.

FMRIB Software Library v0

Windows FSL is not running under Windows. In the GUI there are nine popular modules are defined, and depending on the input file types, they fall into functional-oriented, structural-oriented or diffusion-oriented modules.

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Afterwards you will get a message, that your terminal will accept fsl-commands. Therefore, if you have discovered workflows and methods that fit your data well to best improve SNR, this would be ideal.

Also if you would like to update this page with any particulars for your methods, please let us know and we would be happy to work in additional options.

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It uses least-square fitting to determine the tensor and will output FA and V1 primary eigenvector needed for future analyses.

By preprocessing, we are referring to converting your images from the raw DICOM to FA images for each subject and quality controlling along the way to remove scans with abnormalities and artifacts.

If you have FA measures maps calculated and registered already, we can work with you to include them into the Pipeline rather than to re-run everything from the start. User GUI[ edit ] Just type fsl in the console and get access to the main GUI, from where you could reach to the modules by clicking on the options.

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This will allow maximal integration with current pipelines and ensure optimal processing per site if available, and allow sites to: If not, slight variations in processing will be needed. Most tools will also output FA, MD, and eigenvalue and vector maps simultaneously.

Beginner: Connectome pipeline (MRtrix3, FSL and Freesurfer) - MRtrix3 Community

Multiple acquisitions can be merged for optimal signal-to-noise ratio. Make sure skull-stripping has been performed on both b0 and T1-weighted scans. On the left the orientations are correct, while on the right they are incorrectly aligned and overlaid on b0, not FA!

Calculate tensors this can be done in multiple ways depending on your data. FSLView as the display tool could be completely separate use from processing and analysis. The deformation fields from the warping should then be applied to all volumes in the DWI.

A basic series of steps are as follows: FSL will run perfectly under a vitual machine like VMware Player [1] or VirtualBox [2] Mac OS X no prior steps needed If you want to jump to specific modules directly, then just type in the name starting with a capital letter, e.

How many b0s do you have and where are they with respect to the full series? Linear registration of b0 of DWI and T1-weighted reference together. There can be several ways to pre-process your diffusion weighted data in order to maximize the quality and efficiency of your processing. Melodic for Melodic ICA Melodic Command-line[ edit ] If you want to launch a function from the command line, just type the function name in lowercase, along with the necessary arguments to the function.

If you have already processed your data, please email support.