FSL News

2015 FSL Course: 8-12 June, Waikiki Beach, Hawaii, USA

Mark Jenkinson — Fri, 20 Feb 2015 3:25:11 GMT

We are pleased to announce that the 2015 FSL Course is open for registration.

The course will be held 8-12 June, at the Marriott Resort Waikiki Beach, in Honolulu, Hawaii, USA. This is the week before the OHBM conference in Honolulu.

Both new and existing users of FSL are welcome on the course as it aims to cover both basic and advanced features of FSL.

Numbers of attendees are strictly limited and are available on a first-come-first-served basis.
For further information and to register for the course, please go to:
http://www.fmrib.ox.ac.uk/fslcourse/current.html

Please note that the FSL Course is totally separate from the Exploring the Human Connectome course, although both will be run in the same venue on the same days. The two courses are independent and self-contained, and it will not be logistically possible for attendees to attend sessions from both courses.

For all other information about the course please visit the 2015 course website.

We hope to see you in Hawaii!
FSL Course organisers

2013 FSL & FreeSurfer Course

Mark Jenkinson — Tue, 05 Mar 2013 6:20:19 GMT

We are pleased to announce the 2013 FSL & FreeSurfer Course, to be held in Redmond, WA, USA (June 10-14). It will run the week before the HBM conference, which will be in Seattle, WA, USA.

The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to analyse their own FMRI and MRI data sets.

The course lasts 5 days, from June 10-14, 2013.

Numbers of attendees are strictly limited and are available on a first-come-first-served basis.

For full information and to register for the course, please go to:

http://www.fmrib.ox.ac.uk/fslcourse/current.html

Regards, course organisers.

FSL 5.0 Released

Matthew Webster — Fri, 07 Sep 2012 2:28:38 GMT

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/

2012 FSL & FreeSurfer Course

Mark Jenkinson — Mon, 28 Nov 2011 12:24:38 GMT

We are pleased to announce the 2012 FSL & FreeSurfer Course, to be held in Auckland, New Zealand (May 14-18). It will run immediately after the ISMRM conference, which will be in Melbourne, Australia.

The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to analyse their own FMRI and MRI data sets.

The course lasts 5 days, from May 14-18, 2012.

Numbers of attendees are strictly limited and are available on a first-come-first-served basis.

For full information and to register for the course, please go to:

http://www.fmrib.ox.ac.uk/fslcourse/current.html

Regards, course organisers.

FSL 4.1.9 released

Mark Jenkinson — Fri, 18 Nov 2011 4:15:33 GMT

FSL 4.1.9 has been released:

A large number of minor patches, corrections, documentation updates and compatibility ( for compilation/building ) fixes.

Slice-timing correction in FEAT should be much more accurate.

The full distribution can be downloaded from

http://www.fmrib.ox.ac.uk/fsldownloads/

while incremental patches from 4.1.8 and 4.1.x can be downloaded from

http://www.fmrib.ox.ac.uk/fsldownloads/patches

A patch for Debian/Ubuntu is also available, courtesy of Michael Hanke.

FSL 4.1.8 Released

Matthew Webster — Thu, 14 Jul 2011 7:05:02 GMT

15/05/11 Minor bug fix release
There have been some improvements to the initialisation routines in xfibres
An issue with the -e option in randomise has been resolved - please see the randomise documentation for more details.
A bug in the --peakdist option in cluster has been fixed.

The 2011 FSL & FreeSurfer Course

Matthew Webster — Thu, 24 Feb 2011 3:39:31 GMT

We are pleased to announce the 2011 FSL & FreeSurfer Course, to be held in Montreal, Canada. It will run immediately before the Human Brain Mapping conference, which will be in Quebec City, a short plane/train/road journey from Montreal.

The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to analyse their own FMRI and MRI data sets.

The course lasts 5 days, from June 20-24.

Numbers of attendees are strictly limited and are available on a first-come-first-served basis.

For full information and to register for the course, please go to:

http://www.fmrib.ox.ac.uk/fslcourse/montreal2011.html

Regards, course organisers.

2010 FSL and Freesurfer Course

Matthew Webster — Wed, 03 Feb 2010 1:30:44 GMT

We are pleased to announce the 2010 FSL & FreeSurfer course in
Heidelberg, Germany. It will run immediately before the Human Brain
Mapping conference, which will be in Barcelona - a 2-hour flight from
the Heidelberg area. The course is an official satellite meeting of
the HBM conference.

The course lasts 5 days, from May 31 to June 4.
Numbers of attendees are strictly limited and are available on a first-
come-first-served basis.

For full information and to register for the course, please go to:

http://www.fmrib.ox.ac.uk/fslcourse/heidelberg2010.html

FSL 4.1.5 Released

Matthew Webster — Fri, 29 Jan 2010 10:58:14 GMT

Minor bug fix release
An issue with Randomise "pausing" has been fixed.
The Posterior Insula has been added to the Juelich cyto-architectonic atlas, courtesy of Simon Eickhoff.
There are some improvements to the bedpostx monitor script.
Large speedup for invwarp by automatically adjusting the useful FOV internally (no cropping of the original images needed).

FSL 4.1.4 Released

Matthew Webster — Thu, 11 Jun 2009 1:57:01 GMT

FIRST has a number of changes - it is recommended to rerun previous analyses with this version.
An issue with abnormal termination of FLAMEO on 32-bit systems has been resolved.
There are minor bug fixes to FEAT and FSLView.
The FAST gui now has an additional bias-field option.
The tbss_sym script has been added to TBSS.
There are some small documentation changes.