I have previously used the command eddy_correct which usually took 20 min to complete the processing.

However, I switched to the latest FSL version. Therefore, completed top-up and used the eddy command (described below) after top-up.

eddy --imain=SKY01104.nii.gz --mask=hifi_nodif_brain_mask --index=index.txt --acqp=acqparams.txt --bvecs=bvecs --bvals=bvals --fwhm=0 --topup=topup_AP_PA_b0 --flm=quadratic --out=eddy_unwraped_images

However, this command almost took 4 hours to complete. I am using a Mac with following specifications to run the analysis:

yes, eddy will take a lot longer to run. The upside is that it also gives much better results.

I am not sure what version of FSL you are using, but for more recent versions there is a choice between two executables named eddy_openmp and eddy_cuda. If you have access to an Nvidia GPU you can use the latter, and that will run much faster.

Jesper

Model Name: MacBook Pro

Processor Name: Intel Core i5

 Processor Speed: 2.9 GHz

 Number of Processors: 1

 Total Number of Cores: 2

 L2 Cache (per Core): 256 KB

 L3 Cache: 3 MB

  Memory: 16 GB

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Avantika Mathur

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