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
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