Dear Jesper,
would you then advice to refrain from using --repol with the current
release, and - if one uses it - which is the eddy-corrected output >with<
outliers removed?
(Ruskin seems to indicate that data_eddy.nii.gz appears the eddy-corrected
output without outlier removal while
data_eddy.eddy_outlier_free_data.nii.gz does not appear to be corrected
for eddy currents.)
Hope all is well,
cheers-
Andreas
Am 26.02.15 12:03 schrieb "Jesper Andersson" unter
<[log in to unmask]>:
>Dear Ruskin,
>
>that misreporting is due to a bug in the reporting itself where the
>numbers reported are between the predictions and the predictions of the
>previous iteration, rather than between the predictions and the
>observations. It still uses the correct numbers (which should be above 4
>with the default settings) for the decisions.
>
>Having said that, I would be a little careful with using the outlier
>functionality just yet. A lot of work has gone into that since the last
>release and we are now attempting to properly validate it.
>
>Jesper
>
>On 25 Feb 2015, at 15:29, R Hunt <[log in to unmask]> wrote:
>
>> 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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