I see (after trying it) that --repol produces the following output for --out=data_eddy:
1. data_eddy.nii.gz
2. data_eddy.eddy_parameters
3. data_eddy.eddy_outlier_free_data.nii.gz
4. data_eddy.eddy_outlier_report
However, I'm confused by the output.
File 1 appears to be eddy corrected output, but I assume that it has not had any outliers removed. Am I correct?
File 3 does NOT appear to have been eddy corrected and seems identical to the --imain input data. Am I correct about this as well?
File 4 lists all outliers as being less than +/-0.25 "standard deviations off". Are these slices actually outliers? If so, how is this reflected in the SD value?
Slice 3 in scan 50 is an outlier -0.0149151 standard deviations off
Slice 8 in scan 38 is an outlier -0.0440188 standard deviations off
Slice 8 in scan 91 is an outlier -0.0904612 standard deviations off
Slice 13 in scan 52 is an outlier 0.245672 standard deviations off
Slice 36 in scan 114 is an outlier -0.00400951 standard deviations off
Can someone explain what's going on?
The full command was:
eddy --imain=data --mask=mask --acqp=topup_datain.txt --index=eddy_index.txt --bvecs=bvecs.bvec --bvals=bvals.bval --flm=quadratic --topup=topup_output --out=data_eddy --verbose
Thanks,
Ruskin
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