Just wanted to say thanks for the continuous work and effort put into
this great package! Special thanks go to the NeuroDebian team
(=Michael Hanke) for providing us lazy Ubuntu users with such an easy
way of maintaining the software :-)
Cheers,
Cornelius
On Fri, Sep 7, 2012 at 11:51 PM, wolf zinke <[log in to unmask]> wrote:
> Hi,
>
> I just tested fslview on a machine running Fedora 16, and everything seems
> to be fine. So maybe there is just a problem with Fedora 17, or there is
> something else wrong with the other machine.
>
> wolf
>
>
> On 09/07/2012 07:00 PM, Mark Jenkinson wrote:
>>
>> Hi Wolfe,
>>
>> We'll look into this.
>> In the meantime there's nothing wrong with using the old version.
>>
>> All the best,
>> Mark
>>
>>
>> On 7 Sep 2012, at 16:39, wolf zinke <[log in to unmask]> wrote:
>>
>>> Hi again,
>>>
>>> Funny thing. I thought that there was a conflict with LD_LIBRARY_PATH
>>> which included also the path to vmtk libraries. So I added 'unset
>>> LD_LIBRARY_PATH' as first call in the fslview script to ensue, that only the
>>> FSL libraries got included in this path variable. Now I can sometimes start
>>> fslview, but more often it is causing segmentation faults. It seems like the
>>> first call from a new shell is now successfull, but that for subsequent
>>> calls the likelihood for segmentation faults increase.
>>>
>>> Are there any changes that make it recommended to use this version of, or
>>> would it be an ad hoc solution to run fslview from the previous FSL version?
>>>
>>> btw, when running fslview_bin directly it complains about not finding
>>> libqwt.so.4, so this seems not to be a solution.
>>>
>>> thanks,
>>> wolf
>>>
>>> On 09/07/2012 05:01 PM, wolf zinke wrote:
>>>>
>>>> Hi,
>>>>
>>>> Thanks for the new release. I understand now well the need for the FSL
>>>> course in Bristol - to late though for me ...
>>>>
>>>> I am afraid that now the current Fedora distribution is also getting
>>>> troubles with fslview. It is right now just causing a segmentation fault:
>>>>>
>>>>> fslview
>>>>> /usr/local/fsl/bin/fslview: line 6: 20431 Segmentation fault (core
>>>>> dumped) ${FSLDIR}/bin/fslview_bin $@
>>>>
>>>> I do not know yet if this is caused by some library conflicts since the
>>>> error is not that informative, but I try to figure it out.
>>>>
>>>> Thanks,
>>>> wolf
>>>>
>>>>
>>>> On 09/06/2012 06:56 PM, Matthew Webster wrote:
>>>>>
>>>>> Hello,
>>>>> 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/
>>>>>
>>>>> Many Regards
>>>>>
>>>>> Matthew
>>>>>
>>>>>
>>>>> --------------------------------
>>>>> Dr Matthew Webster
>>>>> FMRIB Centre
>>>>> John Radcliffe Hospital
>>>>> University of Oxford
--
Cornelius Werner
cornelius.werner<at>gmail.com
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