Hi Markus,
I found two possible answers:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=FSL&P=R70380
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=FSL&P=R72421
Good luck,
Roger
Quoting Markus Gschwind <[log in to unmask]>:
> Dear Gwenaelle,
>
> I would then intersect each ROI of the atlas (see previous posts on this)
>> with your mask of significant results, e.g.:
>> fslmaths mymask -mas uncinate mymask_unc
>>
>
> Could you please explain a little more in detail how to create this ROI of
> the atlas (e.g. "uncinate" )
>
> Would I have to extract first each of the tracts
> (from $FSLDIR/data/atlasses/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz)
> and then threshold (at which level?) and create a separate atlas_tract_file?
> Or is there any more sophisticated elegant to do this?
>
> Thank so much!
> Best,
> Markus
>
>
>
> 2010/3/8 Gwenaëlle DOUAUD <[log in to unmask]>
>
>> Hi Roger,
>>
>>
>> > 1. Is there any way to use the cluster program (or
>> > any other program in
>> > FSL) to capture both MNI coordinates and corresponding mean
>> > FA values (for
>> > patient and control groups) of ALL voxels that are
>> > significantly different
>> > between the compared groups?
>>
>> You can use fslmeants on your mean FA map, using a mask that you can create
>> by thresholding/binarising your significant results, e.g.:
>>
>> fslmaths -i tfce_corrp_tstat1 -thr 0.95 -bin mymask
>> fslmeants -i mean_FA -m mymask -o all_voxels_significant.txt --showall
>>
>> > 2. Can a report be generated listing the
>> > total count of significantly
>> > different voxels for each involved white matter structure,
>> > as identified by
>> > the voxels’ MNI coordinates and corresponding labels in
>> > the JHU White-Matter
>> > Tractography Atlas?
>>
>> I would then intersect each ROI of the atlas (see previous posts on this)
>> with your mask of significant results, e.g.:
>> fslmaths mymask -mas uncinate mymask_unc
>>
>> To get the number of voxels, just do a fslstats -V on each of your new
>> masks.
>>
>> > 3. Can mean FA also be calculated (for patient and
>> > control groups) for
>> > these significantly different voxels grouped by white
>> > matter structure?
>>
>> Just repeat the fslmeants command above with the appropriate new masks.
>>
>> Hope this helps,
>> Gwenaelle
>>
>>
>>
>>
>
>
> --
>
>
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition - Dept of Neurosciences
> University Medical Center (CMU)
> 1, Michel-Servet
> CH-1211 GENEVA - Switzerland
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
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