You can do something like : fslmaths <tbss_skeleton> -mas
<original_slf_mask> -bin tbss_skeleton_slf_only_mask
On Tue, Nov 18, 2014 at 2:28 PM, André Schmidt <[log in to unmask]> wrote:
> Ok, that's probably the reason why the values are so low. Sorry for asking again, but how can I create a mask of the TBSS skeleton with the SLF mask?
>
> BW
> andre
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]]" im Auftrag von "Niels Bergsland [[log in to unmask]]
> Gesendet: Dienstag, 18. November 2014 13:32
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] AW: [FSL] AW: [FSL] AW: [FSL] Calculating the skeleton white matter mean FA
>
> One potential issue there is that fslmeants gives you the mean of ALL
> voxels in the mask (including voxels with a value of zero). So in case
> you haven't already done that, you will need to first create a mask of
> the TBSS skeleton with the SLF atlas, and then provide that result as
> the option to -m (and as Steve said earlier, you may perhaps want to
> dilate the tract mask beforehand.
>
> On Tue, Nov 18, 2014 at 1:12 PM, André Schmidt <[log in to unmask]> wrote:
>> Hi,
>>
>> Great, thank you, this works well. In order to extract individual's FA value in the SLF, I am correct doing the following:
>>
>> e.g. for the temporal part of the SLF: fslmeants -i all_FA_skeletonised -m SLFtemporalpartR
>>
>> Thank you very much.
>> BW
>> Andre
>> ________________________________________
>> Von: FSL - FMRIB's Software Library [[log in to unmask]]" im Auftrag von "Niels Bergsland [[log in to unmask]]
>> Gesendet: Dienstag, 18. November 2014 12:23
>> An: [log in to unmask]
>> Betreff: Re: [FSL] AW: [FSL] AW: [FSL] AW: [FSL] Calculating the skeleton white matter mean FA
>>
>> Hi - the easiest point and click way to do it is via fslview by
>> enabling the atlas tools, clicking the Structures button, and then
>> changing to the JHU atlas, selecting your structure of interest,
>> enabling "Preview selected structures' probability map" and then
>> saving it from fslview. You can also do this all from the command line
>> with the appropriate commands, but if you are unsure about that, the
>> safest thing is just from within fslview as I described.
>>
>> On Tue, Nov 18, 2014 at 12:08 PM, André Schmidt <[log in to unmask]> wrote:
>>> Hi,
>>>
>>> Thank you. I see all the files in the JHU folder and that the SLF is indexed with 14, 15, 18 and 19 (as described in the JHU-tract.xml file). But I don't know how I can extract a mask from these files (which one exactly) which only contains the SLF - can you please tell me how to do this?
>>>
>>> Many thanks in advance for your help.
>>> Andre
>>> ________________________________________
>>> Von: FSL - FMRIB's Software Library [[log in to unmask]]" im Auftrag von "Niels Bergsland [[log in to unmask]]
>>> Gesendet: Dienstag, 18. November 2014 10:08
>>> An: [log in to unmask]
>>> Betreff: Re: [FSL] AW: [FSL] AW: [FSL] Calculating the skeleton white matter mean FA
>>>
>>> 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
>>> [log in to unmask]
>>
>>
>>
>> --
>> Niels Bergsland
>> Integration Director
>> Buffalo Neuroimaging Analysis Center
>> 100 High St. Buffalo NY 14203
>> [log in to unmask]
>
>
>
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]
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