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Dear Jesper,

Thank you very much for a response. Actually, I omitted one 1 in the index file as I'm not familiar with the zero-based index. It's running now. sorry for a false alarm.

Is the number in the fourth column really irrelevant when there is only one row? Or would it help if it's accurate?

---
Seung-Goo KIM

On Mon, Aug 7, 2017 at 12:04 PM, Jesper Andersson <[log in to unmask]> wrote:
Dear Seung-Goo,


I am trying to analyze DWI data without any means to correct susceptibility-induced distortion (no field map, no inverse phase-ecndoing). I hope "eddy" outperforms "eddy_correct", but the "eddy" does not run without "acquisition parameters" and "index". 

I thought I could run it with just a [1x4] vector (for one phase-encoding) in the "acquisition parameter file" and all 1's (as many as the number of volumes) in the "index file", but it returns

I am guessing that you mean that your acqp file looks something like

0 1 0 0.05

in which case that should work.  The error message below isn’t really much help, and also a bit surprising since I don’t think I throw any exceptions without a proper explanatory message.

Can you maybe try to run again, and this time include --very_verbose at the end of the command and cut and paste the screen output to an email to me?

Jesper


exceptions:

$ eddy --imain=dwi.nii --mask=brain_mask.nii --bvecs=bvecs --bvals=bvals --out=data --acqp=acqp --index=index


terminate called after throwing an instance of 'EDDY::EddyException'
  what():  pǙ;
Aborted

Could anyone please share a tip on this issue? 

Best regards,
-- 
Seung-Goo Kim
Doctor of Natural Science in Psychology

Research Group for Cortical Networks and Cognitive Functions,
Max Planck Institute for Human Cognitive and Brain Sciences,
Stephanstrasse 1A, 04103 Leipzig, Germany.
Phone: +49 341 9940 2618 | Fax: +49 341 9940 2624
http://www.cbs.mpg.de/~skim