Hi again Jack,
something about your data just struck me.
If you are using the b02b0.cnf file "as is” you are essentially asking for warp-fields with a resolution (knot-spacing) of several tens of mm for the early iterations. But you have an FOV of ~200*0.01=2mm. I think that is most likely the problem.
I am guessing these are mice or some even smaller animal? What I usually recommend in those cases is to “fake” an object of roughly the size of the human brain by multiplying the voxel size by some suitable factor, in your case that would be ~100. I think if you do that things will work.
Jesper
> On 1 Mar 2017, at 21:41, Jack Grinband <[log in to unmask]> wrote:
>
> Hi All,
> I'm getting a segmentation error when running topup. It doesn't seem to be a memory issue -- I have 32G RAM and it only uses 20G before crashing. Are there any matrix or voxel size restrictions on the input to topup?
> thanks,
>
> jack
>
>
> Output of fslsize:
> dim1 284
> dim2 190
> dim3 84
> dim4 2
> pixdim1 0.010000
> pixdim2 0.010000
> pixdim3 0.030000
> pixdim4 6.000000
>
>
> Platform:
> FSL 5.0.9
> OS X 10.11.6
>
>
> Command:
> topup --imain=myfile --datain=params.txt --config=b02b0.cnf --out=unwarped_results --fout=field --iout=unwarped
>
>
> Error:
> Segmentation violation, Address not mapped, Offending address = 0x6e008e000
> topup 0x000000010006d258 BASISFIELD::Spline3D<double>::common_construction(unsigned int, std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<unsigned int, std::allocator<unsigned int> > const&)
> topup 0x0000000100061d77 BASISFIELD::splinefield::splinefield(std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<double, std::allocator<double> > const&, std::vector<unsigned int, std::allocator<unsigned int> > const&, int)
> topup 0x000000010000f01b TOPUP::TopupCF::field_factory(NEWIMAGE::volume4D<float> const&, double, unsigned int) const
> topup 0x0000000100010b5d TOPUP::TopupCF::TopupCF(NEWIMAGE::volume4D<float> const&, NEWMAT::Matrix const&, NEWMAT::ColumnVector const&, double, unsigned int)
> topup 0x000000010003670e main
> topup 0x00000001000016b8 start
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