Yes,
the “regular” output is corrected for everything you “ask for” on the command line.
Jesper
On 26 Feb 2015, at 19:28, Andreas Bartsch <[log in to unmask]> wrote:
> Hi Jesper,
>
> thanks a lot. Excellent.
> But just one more question: So is the regular output data_eddy.nii.gz eddy
> corrected WITH outliers removed?
> Thanks again.
> Cheers,
> Andreas
>
> Am 26.02.15 17:00 schrieb "Jesper Andersson" unter
> <[log in to unmask]>:
>
>> Hi Andreas,
>>
>> yes, I think it would probably be wise to be very careful with using the
>> current release. If for no other reason that it will be hard to convince
>> reviewers given that there is no paper validating it published yet. I
>> thought I had hidden the help text for the <repol option, but clearly I
>> must have missed that.
>>
>> And yes you are correct, the *.eddy_outlier_free_data.nii.gz file is the
>> one where *only* outlier replacement has been done whereas the regular
>> output is the one where everything has been done.
>>
>> Jesper
>>
>> On 26 Feb 2015, at 14:21, Andreas Bartsch <[log in to unmask]> wrote:
>>
>>> 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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