On 17 Nov 2018, at 08:39, Niklas Lenfeldt <[log in to unmask]> wrote:

Thanks. it is very strange. Some of the data that yielded a segemenation error first...now went through the entire loop without any problem

and the error does not only occur the first time, it can be another iteration.

so I do not think there is an error in the b-files. I have checked with dtifit that L1 fits with the fibers. Not for all data but the dicom to nifti conversion is the same for all data.

when is the new eddy due?

best nick

Niklas Lenfeldt, PhD, MSc E.P
Umeå University
Phone: +46706096687

________________________________________
Från: FSL - FMRIB's Software Library <[log in to unmask]> för Jesper Andersson <[log in to unmask]>
Skickat: den 9 november 2018 15:06
Till: [log in to unmask]
Ämne: Re: [FSL] segmentation error

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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