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.
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
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)