Take a look at the JHU WM Tractography atlas. Both of those are in there.
On Tue, Nov 18, 2014 at 9:53 AM, André Schmidt <[log in to unmask]> wrote:
> Hi,
>
> Thank you. Is there a good mask for the SLF (and corticospinal) available in
> fsl/data/atlases, or do I need to create one by myself?
>
> Thanks again.
> BW
> Andre
> ________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]]" im Auftrag von
> "Stephen Smith [[log in to unmask]]
> Gesendet: Dienstag, 18. November 2014 09:24
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] Calculating the skeleton white matter mean FA
>
> Hi - sure you can always use tract-specific masks by intersecting (eg) atlas
> tract masks (potentially dilated) with the mean FA skeleton mask.
> Cheers
>
>
>
> On 18 Nov 2014, at 08:21, André Schmidt <[log in to unmask]> wrote:
>
> Dear Steve,
>
> I had the same question in mind, thanks for the hint. I guess this will
> provide each subject's "global" FA value - is there even a way to get these
> values depending on the specific WM tracts?
>
> Thanks for your help.
> André
> ________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]]" im Auftrag von
> "Stephen Smith [[log in to unmask]]
> Gesendet: Dienstag, 18. November 2014 09:14
> An: [log in to unmask]
> Betreff: Re: [FSL] Calculating the skeleton white matter mean FA
>
> Hi - it's simpler than this - just run a full default TBSS fed from all
> subjects in one analysis - and then take all_FA_skeletonised and summarise
> that per subject:
>
> fslmeants -i all_FA_skeletonised -m mean_FA_skeleton_mask
>
> Cheers.
>
>
>
>
> On 18 Nov 2014, at 02:26, M. alshikho <[log in to unmask]> wrote:
>
> Dear Mark,
> I Have a suspicion that my question is not posted before so I am posting it
> again!
>
> I have two groups of subjects. I ran the TBSS analysis and I got the results
> after running the randomise command line.
> Now if I want to calculate the mean FA on the subject's skeleton (for every
> subject). Is it valid to generate a skeleton for the white matter for every
> subject by running the TBSS scripts (1---> 4) for the subjects one by one
> i.e running the TBSS scripts on one subject every time ? then by running the
> following command line (fslstats -t all_FA -k mean_FA_skeleton_mask -M) I
> can calculate the mean FA on the skeleton for every subject?
>
> I highly appreciate your opinion and any other ideas!
> Thanks
>
>
>
> ---------------------------------------------------------------------------
> 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] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
>
>
> ---------------------------------------------------------------------------
> 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] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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