Dear Jakub,
it seems you get stuck at the first time you load the prediction maker for the dwi:s (the first iterations you see there are for the b0:s). I can’t say based on the below why that is. If you change -v to --very_verbose there will be more information that might help.
I am also a little concerned that your cost function value increases after the first iteration for the b0.
If we still can’t figure it out after that I will need to take a look at the data myself. But I won’t be able to do that until I am back after ISMRM.
Jesper
> On 19 Apr 2017, at 22:46, Jakub Zimolka <[log in to unmask]> wrote:
>
> Hello,
> I have dMRI resolve dataset of 26 subjects. The dataset resolution is 220x110x15, with 63 diffusion weighted images and 7 b0 images in AP and 5 b0 images in PA phase encoding. Total 12 (7+5) b0 images enters topup. Output of topup enters eddy, also merged AP+PA acquistion images (63+7+5) enters eddy, then bvecs, bvals etc...
> For some subject this preprocessing works well (total duration for example 1-2 hours). However for about half of subject it get stuck at eddy. When I turn on diagnostic messages (--verbose) it gets to "evaluating prediction maker model" after 10 minutes of computing and nothing more. The same message is there after 12 hours.
> I am now wondering why it get stucked, because for some subjects it is working really well. Could anyone please help me?
>
> Here is the output:
>
> eddy_openmp --imain=eddy_input_resolve.nii.gz --mask=mask_r.nii.gz --index=index.txt --acqp=acq_file_resolve.txt --bvecs=eddy_input_resolve.bvec --bvals=eddy_input_resolve.bval --topup=topup_resolve --out=eddy_resolve -v
>
> Reading images
> Running Register
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 0, Total mss = 1015
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 1, Total mss = 998.511
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 2, Total mss = 1051.58
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 3, Total mss = 1056.69
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 4, Total mss = 1056.6
> Running sm.Setb0Reference
> Running sm.PolateB0MovPar
> Running Register
> Loading prediction maker
> Evaluating prediction maker model
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