[Neuroimaging] Scrubbing DTI images

[Samuel St-Jean]

Denoising will give you back plausible values based on neighborhood
information, it will not do whole volume rejection, restore will do that
for you though based on the tensor model.
On May 18, 2016 8:53 AM, "Mahmoud" <zeydabadi at gmail.com> wrote:

> Thank you all for the hints.
>
> Oscar,
> Could you elaborate more about what you suggested? I mean what exactly
> denoising is doing?
>
> Thank you!
> Mahmoud
>
> On Tue, May 17, 2016 at 4:43 PM, Oscar Esteban <code at oscaresteban.es>
> wrote:
>
>> Hi Mahmoud,
>>
>> Just to add some to Chris' response. RESTORE will fit the DTI rejecting
>> outliers "voxel-wise".
>>
>> Probably you want first to run something like FSL Eddy (
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY/UsersGuide). Eddy will deal
>> with head motion, eddy currents and susceptibility distortions. One
>> approach to remove outliers is denoising, i.e. using
>> http://nipy.org/dipy/examples_built/denoise_nlmeans.html
>>
>> If you do not denoise, RESTORE may a good option if you want to fit DTI.
>>
>> Cheers,
>> Oscar
>>
>> On Tue, May 17, 2016 at 1:34 PM, Chris Filo Gorgolewski <
>> krzysztof.gorgolewski at gmail.com> wrote:
>>
>>> You should look into RESTORE which fits DTI with outliers removed/down
>>> weighted: http://nipy.org/dipy/examples_built/restore_dti.html
>>>
>>> On Mon, May 16, 2016 at 1:08 PM, Zeydabadinezhad, Mahmoud <
>>> mahmoud.zeydabadinezhad at emory.edu> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I have some DTI images collected in 61 directions + 6 B0s in 3T. I was
>>>> wondering if you could give me a hint how can I do scrubbing on my DTI data
>>>> either using FSL or DIPY or any other script.
>>>> By scrubbing, I mean the same idea used in fMRI community i.e.
>>>> detecting the outlier/motion corrupted slices or volumes and removing them
>>>> from DTI calculation.
>>>> I appreciate your time and help.
>>>>
>>>> Thank you!
>>>> Mahmoud
>>>>
>>>>
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