FSL 5.0 Released Posted By: Matthew Webster - Sep 7, 2012Tool/Resource: FSL We are proud to announce that FSL 5.0 has been released. This is a major release including: • New live Wiki-based documentation • Dual Regression - maps a set of group-ICA spatial maps back into individual subjects' datasets • BASIL - a new suite of tools for the quantification of resting perfusion from Arterial Spin Labeling MRI, including correction for variable bolus arrival time, macro vascular contamination and the effects of partial voluming. • BBR - a new option for EPI to structural registration, which is an implementation of Doug Greve's Boundary-Based-Registration method that includes built-in fieldmap-based distortion correction. This is now the default option for all FMRI to structural registrations as it has been found to be substantially more accurate, and is now built into FEAT and MELODIC registration. • PNM - Physiological Noise Model is a tool for correcting physiological noise, based on cardiac and respiratory recordings (typically, but not restricted to, pulse-ox and bellows). It provides the standard RETROICOR-style regressors as well as additional ones including interactions (cardiac * respiratory), RVT, heart rate. This is strongly recommended to be used in any FMRI studies focussing on the brainstem, spinal cord, or other structures in the inferior part of the brain. • Atlases - Oxford-GSK-Imanova structural and connectivity striatal atlases - two main atlases provided that sub-divide the striatum based on (i) the white matter connectivity to major functional regions of the cortex and; (ii) a structural atlas derived from literature-based rules that subdivides striatum into caudate, putamen and ventral striatum. • FIRST - a new vertex analysis method, based on projection to the average surface normal, that provides (i) a general GLM setup, including arbitrary contrasts; (ii) input images for randomise (not surfaces); and (iii) a new selection of multiple-comparison methods to be employed for vertex analysis. In addition, the old vertex analysis method, with surfaces, remains available. • Fieldmaps - fsl_prepare_fieldmap is a tool designed to make the initial processing of fieldmaps easier (designed for only Siemens scanners currently). It creates the necessary inputs (rad/s map and magnitude) for FEAT processing. • Randomise - Lesion masking - a new script, setup_masks, is supplied to assist in using lesion masks (user-supplied) in randomise to exclude (inconsistently located) lesions from group studies. • Lesion Filling - a new tool for taking structural images and filling lesion areas (specified by user-defined masks, e.g., drawn by hand) in order to improve segmentation and registration performance. • SIENA - a separate ventricle-based analysis is now possible • Probtrackx2 - A new version of the probabilistic tracking tool that includes many more options such as: handling surfaces (from Caret, FreeSurfer and FIRST), mixtures of images and surfaces, matrices output, and more... • Various updates to the FDT GUI. It allows the user to set all the available command-line options • BedpostX - A new model for estimating fibre orientations using multi-shell data is available. Also new options for modelling different noise distributions. • Qboot - A tool for estimating fibre orientations non-parametrically using ODFs (orientation distribution functions). Uncertainty is estimated using residual bootstrap. • Tools for processing surface files, such as surf2volume, surf2surf, surf_proj • fsl_anat (BETA version) - Anatomical Processing Script (BETA version) - a flexible new tool that combines the existing features of brain extraction (BET+FNIRT-based masking), registration (FLIRT + FNIRT), tissue-type segmentation (FAST), subcortical segmentation (FIRST), with substantially enhanced bias-field correction and automatic reorientation and cropping. • topup (BETA version) - A tool for estimating and correcting susceptibility induced distortions • eddy (BETA version) - An advanced, highly tailored and accurate tool for correcting eddy-current-distortions • A large array of minor improvements and additions to tools (e.g. massive speedup to invwarp, fill holes in fslmaths, spline interpolation in flirt, DVARS option in fsl_motion_outliers, ...) We strongly recommend upgrading to this version, only limited support is available for older FSL versions. We now only provide pre-built binaries for 64-bit Centos and Intel-based Mac systems. For other platforms, a build from source is required. Native Debian/Ubuntu builds will be available shortly, courtesy of Michael Hanke. A small number of scripts now use python - these require a python-enabled OS to run. The full distribution can be downloaded from http://www.fmrib.ox.ac.uk/fsldownloads/ |
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