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]
|