Problem with fslview after registration


#1

Hello

I am new to mrtrix and this forum. I am using freesurfer to parcellate a T1 image and FSL FIRST to do the striatum. I am co-registering the freesurfer/FSL output to diffusion space before running mrtrix using niftireg before running mrtrix to generate my connectome.

However when I try to use fslview (version 6.0) to view the registration I get the error below. However fslview still works for all other images and the output image can be viewed on my colleagues mac with his fslview which is the same version so it’s not a problem with the file itself. Could anyone help here? Thanks, Paul

$ fslview diff_space_nodes_fixSGM.nii.gz
fslview_bin: /usr/local/boost_1_33_1/boost/shared_ptr.hpp:253: T* boost::shared_ptr::operator->() const [with T = OverlayList]: Assertion `px != 0’ failed.
/midas-data/software/fsl/bin/fslview: line 6: 22485 Aborted (core dumped) ${FSLDIR}/bin/fslview_bin $@


#2

Hi @uclpz,

That sounds very much like an FSL (fslview) issue then… I suppose you’ll have more luck trying to find answers by asking on the FSL mailing list. :wink:

Cheers,
Thijs


#3

I agree with @ThijsDhollander on this one:

That failed assertion indicates an uninitialised (shared) pointer - this simply shouldn’t happen…

One thing you might want to try is check that fslhd can read the image correctly, just to make sure it is valid NIfTI as far as FSL is concerned. Another thing to try is changing the datatype of the image - I’ve seen instances where certain datatypes caused fslview to crash with similar errors. Try something like this:

$ mrconvert diff_space_nodes_fixSGM.nii.gz -datatype int32 diff_space_nodes_fixSGM_converted.nii.gz

See if that helps… You could also try other datatypes like uint16 (see the list in the help page, under ‘Datatype’, just type mrconvert to display it).


#4

Changing the datatype from uint32 to int32 proved a success. Thank you very much!