Hi Ida,
> Firstly; I confused something and have to correctly say that I do have the vbm.
Ok, that’s good to know.
> To your questions:
>
> - eddy ran without any error and I can open the qc files
> - actually I dont have c_1021_DTI_eddy_corrected.eddy_cnr_maps.nii.gz in my eddy folder - so something went wrong here. Are there any prerequisites so that eddy can compute this?
Not really, other than having enough b0 values to compute SNR maps, otherwise they’ll all be 0.
Which version of FSL are you using? Have you used the --cnr_maps flag when calling eddy?
> - so when telling eddy to output the residuals, I should get the msr.txt and I don't have to change anything about the eddy_quad command?
No, it’ll get the volume-wise average residual value and store it in the msr.txt file.
Cheers,
Matteo
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