tortions using the eddy correct FSL tool (www.fmrib.ox.ac.uk/fsl) for which a gradient table was calculated to account for the distortions. As an image pro-cessing step, DWIs were up-sampled to the resolution of the anatomical images (with isotropic voxels) using FSLs irt function with 9 degrees of freedom; the
Nov 18, 2014 · In the default setting of FSL, eddy_correct uses a trilinear function as an interpolation method and does not have the option selecting other interpolation methods.
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- FSL: eddy_correct, rotate_bvecs • Fit a diffusion model at every voxel - DTK: DSI, Q-ball, or DTI - FSL: Ball-and-stick (bedpost) or DTI (dtifit) • Compute measures of anisotropy/diffusivity and compare them between populations - Voxel-based, ROI-based, or tract-based statistical analysis • For tract-based: Reconstruct pathways

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  • Jun 11, 2020 · Raw diffusion-weighted images were corrected for eddy current distortions using the FSL tool, “eddy_correct”. For each subject, the 11 eddy-corrected images with no diffusion sensitization were averaged, linearly aligned and resampled to a downsampled version of their corresponding T1 image (110 × 110 × 110, 2 × 2 × 2 mm).
  • corrected using the FSL eddy_correct tool (Andersson and Sotiropoulos,

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Launch FSL by typing 'FSL &' from the command line. Press the "FDT Diffusion" button from the main FSL menu to show the diffusion processing window. At the top, select the EDDY CURRENT CORRECTION. Press the folder icon to select the image (e.g. DTI30s010.nii.gz). Also, put in the output name you want to identify it as the corrected data.

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  • Magnetic field inhomogeneities were corrected using epidewarp.fsl. Skull-stripping was performed through FSL’s bet. TRACULA used prior anatomical information derived from cortical parcellation and subcortical segmentation obtained for each subject by processing the individual T 1 -weighted images through FreeSurfer ( http://freesurfer.net/ ).
  • image are significantly different. FSL’s Eddy tool [8] overcomes this issue by using the entire diffusion set to make predictions of how the image contrast should be. Even though this approach has been proven to be superior to the previous eddy_correct [9], its performance is expected to depend on the DWI acquisition scheme.

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Pre processing The 64 and 6 angular direction image data sets were then combined using inhouse software written in IDL, MRI Analysis Software (MAS). The comb ined data was motioncorrected using FSLs Eddy Correct.13 MAS was used to interpolate the data to a 0.85 mm isotropic resolution.

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Steps (all FSL except for rotbvecs, which is custom) 1. (optional) fslmerge. 2. fslroi (get the no diffusion volume) 3. bet (get the brain mask based on the no diffusion volume) 4. eddy_correct (eddy current correction) 5. rotbvecs (rotate bvecs) 6. dtifit (fit the diffusion model to get MD, FA maps etc)

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Due to the contrast differences between each DWI with the b 0 volume, FSL‐eddy_correct's default "inter‐modal" cost function for alignment is a correlation ratio. However, even in the near absence of subject motion, this method produced significantly nonzero registration parameter values (i.e., translations and rotations).

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This is a new tool to correct for eddy current-induced distortions and subject movements. It simultaneously models the effects of diffusion eddy currents and movements on the image, allowing it to work with higher b-value data than has been possible with for example eddy_correct (FSL's earlier tool for eddy current correction).

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使用fsl进行MRI脑图像分析 MED620122 生物医学工程进展 1 安装教程 软件与系统版本 FLIRT version 6.0 Ubuntu 16.04 FSLeyes version 0.31.0+build0(这里有个坑是,fsl本身也自带fsleyes,但是版本较低,有些功能使用会有问题,需要单独下载fsleyes然后替换) 首先,去官网下载 ...

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