Dear Niklas,
it is hard to say exactly what has gone wrong from the messages below. It seems it goes wrong when estimating the parameters for the Gaussian Process for the first time. One possible reason for that can be if there is a mismatch between the information in the bvals/bvecs file and what is actually encoded in the images, i.e. if one has gotten the bvals/bvecs files wrong.
If that is not the problem I would need to take a look at your data myself. But there is no point in me doing that before the 6.0.1 release of eddy, to first see if maybe that fixes your problem.
Jesper
> On 31 Oct 2018, at 09:47, Niklas Lenfeldt <[log in to unmask]> wrote:
>
> while running eddy on a few of my samples, I get a segmentation violation
>
> [niklasl@localhost test]$ ./preproc_eddy3T.txt
> Reading images
> Performing volume-to-volume registration
> Running Register
> Loading prediction maker
> Evaluating prediction maker model
> Segmentation violation, Address not mapped, Offending address = 0x770000006e
> /lib64/libc.so.6 [0x7ff023f2b3c1]
> eddy ) [0x6062eb] [
> eddy ) [0x5ff163] [
> eddy ) [0x45fab5] [K�
> ./preproc_eddy3T.txt: line 4: 21758 Segmentation fault (core dumped) eddy --imain="${katalog}_DTI.nii" --mask="${katalog}_DTI_brain_mask.nii.gz" --acqp="${katalog}_DTI_acqparam.txt" --index="${katalog}_DTI_index.txt" --bvecs="${katalog}_DTI.bvec" --bvals="${katalog}_DTI.bval" --out="${katalog}_DTI_corr" --slm=linear --repol --niter=5 --fwhm=10,0,0,0,0 -v
>
>
> does anyone have an idea? It happens only on a few cases. the rest works fine. have opened them in fsleys and I think they look no worse than other samples.
>
> best
>
> nick
>
>
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