In general, yes, if you think registration to the atlas is very good.
Saad.
On 10 Nov 2011, at 10:09, Garin, Alba wrote:
> Hi Saad,
>
> thanks, it gives some values in the resulting mask. anyway, is that the good way to create a mask for probtrackx?
>
> thanks,
> Alba
> PhD Student
> Simulation Area - Applied Mechanics,
> CEIT - Spain
> ________________________________________
> De: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de Saad Jbabdi [[log in to unmask]]
> Enviado el: miércoles, 09 de noviembre de 2011 20:04
> Para: [log in to unmask]
> Asunto: Re: [FSL] probtrackx - creating a mask for it
>
> Hi Alba
>
> Try with one of the "maxprob" images. For example: JHU-ICBM-tracts-maxprob-thr25-1mm.nii.gz
> The one you were using is a 4D image with concatenated probabilistic tracts.
>
>
> Cheers,
> Saad
>
>
> On 9 Nov 2011, at 11:52, Garin, Alba wrote:
>
>> Good afternoon,
>>
>> i want to do probtrackx for a dataset and i want to do it for a roi. Therefore, i need a mask to define this roi. I thought about doing it with sth like
>>
>> fslmaths /usr/share/fsl/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz -thr 6 -uthr 6 mask-tr6.nii.gz
>>
>> that creates a mask for the area 6 detailed in that atlas. My problem is that it gives a empty mask, and i think it is because the area is small or sth similar.
>> should i specify a input mask for that command?
>> will i have any problem with different spaces? (when doing probtrackx in my dataset?)
>> Could anyone help me? any other way to do it?
>>
>> thanks in advance
>>
>> Alba Garin
>> PhD Student
>> Simulation Area - Applied Mechanics,
>> CEIT - Spain
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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