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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