[Simnibs-discuss] dwi2cond

Axel Thielscher axelt at drcmr.dk
Fri Nov 26 13:46:42 CET 2021


please open the file "dwi2cond", which is in the simnibs/bash_modules 
subfolder of your simnibs installation and change (around line 56)




Best regards,


On 11/26/2021 10:24 AM, Zhen Li wrote:
> Dear researchers,
> When I run codes to prepare DTI images in SimNIBS on Mac:
> dwi2cond --all --eddy --phasedir=-y --readout=0.05 ernie 
> org/ernie_dMRI.nii.gz org/ernie_dMRI.bval org/ernie_dMRI.bvec 
> org/ernie_dMRI_rev.nii.gz
> The error shows mainly like this:
> *eddy: msg=--rep_ol cannot be used for this version of eddy*
> but for the given patch here : 
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Patches,
> there is no other version as its recommendation:*e.g. 5.0.0 to 5.0.2*
> I can only download *5.0.9 to 5.0.X or **5.0.9 to 5.0.8*.
> I am not sure if it is to do with the version issue.
> Could you please help me with that?
> I appreciate it😊.
> Best regards,
> Zhen
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Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
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