Hi Sven,
Do you have a dual echo ASL acquisition? If you have a more typical
single echo ASL acquisition, then FABBER doesn't have an appropriate model
for computing quantitative CBF. In which case, if you want quantitative
CBF, there is to my knowledge no tool for doing that within FSL. There is
an SPM-based toolbox from the UPenn group that you might want to look
into:
http://www.cfn.upenn.edu/~zewang/
cheers,
-MH
> Dear Steve
>
> Thanks a lot
>
> I looked at the documentation of FABBER, and tried some things, yet I am
> not sure that I am doing the right thing and the documentation is a little
> coarse....
>
> I have a 4D dataset which I converted from dicom into nifti
> 105 scans
> alternating tagged and reference images
> TR 4000
>
> I do not want to specify any time-course of activations, I simply want to
> estimate the relCBF parameter
>
> Could you please indicate which command I should use?
>
> Thanks a lot
> Sven
>
> On 20 mars 2012, at 09:29, Stephen Smith wrote:
>
> Hi - depending on exactly what your ASL data contains, you may benefit
> from running FABBER - see the documentation.
> Steve.
>
>
> On 20 Mar 2012, at 08:24, HALLER Sven wrote:
>
> Dear Najmeh and Andreas
>
> Thanks a lot for your messages, even though I must admit that I was hoping
> for a more straightforward and simple analysis ...
>
> Another question: Is it possible to do the relCBF ASL "fit" in FSL?
> I am asking because at least visually, the FA maps calculated in FSL
> DTIFIT outperform the FA maps calculated on the SIEMENS scanner. In the
> same line I am wondering as to whether or not the ASL relCBF maps in FSL
> might be better than the SIEMENS maps
>
> Thanks a lot
>
> Sven
>
> On 19 mars 2012, at 12:36, Andreas Bartsch wrote:
>
> Hi Sven,
>
> if you do have M0 calibration scans you >could< try to calculate absolute
> perfusion values, merge these across sessions / subjects and use these as
> a 4D confound.
> However, usually the z-coverage of ASL is below that of the BOLD
> acquisitions, i.e. you may need to cut down your analysis to the partial
> volume of the ASL. Furthermore, if you don't have the calibration scans
> you are lost.
> You may consider to extract some reference ratios but I'm afraid there is
> no region where you could safely assume that caffeine has no effect upon
> it.
> Hth,
> Andreas
>
> Am 19.03.12 11:56 schrieb "HALLER Sven" unter
> <[log in to unmask]<mailto:[log in to unmask]>>:
>
> Dear FSL expert
>
> I have a study aiming to assess the effect of caffeine on working memory
>
> I have a 2back working memory task. In a repeated measures design, each
> subject performs 2 days (one with placebo, one with caffeine), and 2
> 2back tasks each day (total of 2x2 fMRI EPI BOLD runs per subject).
>
> The problem is that caffeine has a direct vascular effect. To capture
> this, each subject additionally has an ASL on each day. The idea is to
> assess the global CBF changes in ASL, and to eliminate this effect from
> the fMRI EPI BOLD analysis.
>
> I looked into the FEAT analysis, and there is in fact a perfusion
> analysis. Yet if I understood correctly, this analysis is rather intended
> for fMRI-like analysis of ASL instead of EPI data.
>
> Are there any suggestions how I could use the ASL data to extract
> medication-related changes in CBF from the fMRI tasks??
>
> Your help is highly appreciated
>
> Sven
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask]<mailto:[log in to unmask]>
> http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
>
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