SyN Registration Error

Submitted by nkraus on

We are currently running DIFFPREP on some data we have collected. We are running the DIFFPREP function (TORTOISE V3.2.0) on Linux  on Ubuntu 20.04.  Below is our currently input:

DIFFPREP --dwi ~/Desktop/Tortoise_DTI/Tortoise/1007/diffusion_data.nii --bvecs ~/Desktop/Tortoise_DTI/Tortoise/1007/bvecs  --bvals ~/Desktop/Tortoise_DTI/Tortoise/1007/bvals -p vertical -s ~/Desktop/Tortoise_DTI/Tortoise/1007/T2_acpc.nii --unsampling all --keep_intermediate 0


The process gets "Killed" when running the 4 of 4 levels of the SyN registration. I have included a screenshot of levels 3/4 and 4/4 where the function is killed. Originally, we tried this with a structural image that was gzipped (T2_acpc.nii.gz). The same error appeared when we used the .nii.gz file and the .nii file for the structuralT2 image. Are there any reasons why these files would result in this error? Is there any checks on each file I can complete in order to ensure that this error does not occur and the DIFFPREP function can be completed properly?


Thank you.

Submitted by irfanogl on Mon, 10/18/2021 - 09:26




First of all, I suggest to to provide the tags "--unsampling all --keep_intermediate 0"  .  These are still present for legacy reasons.

Coming back to your question.

There are two reasons why it could crash at that part: 1) Insufficient memory  2) Something went wrong beforehand.

Even 8GB RAM should be enough for that part so I suspect it is the latter. Especially looking at the metric values at the 3rd level. These metric values do not make sense.  Maybe the rigid registration of the structural to the b=0 image failed beforehand?  Can you copy the contents of log_structural_to_b0_rigid.txt  in the log folder too?   What happens if you dont do EPI distortion correction? (by setting --epi off)