[Neuroimaging] Scrubbing DTI images

[Mahmoud]

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
>>>
>>>
>>> ------------------------------
>>>
>>> This e-mail message (including any attachments) is for the sole use of
>>> the intended recipient(s) and may contain confidential and privileged
>>> information. If the reader of this message is not the intended
>>> recipient, you are hereby notified that any dissemination, distribution
>>> or copying of this message (including any attachments) is strictly
>>> prohibited.
>>>
>>> If you have received this message in error, please contact
>>> the sender by reply e-mail message and destroy all copies of the
>>> original message (including attachments).
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20160517/92e7026a/attachment.html>