Thanks a lot.
Best Regards
Jiansong
===============
Jiansong Xu, M.D., Ph.D.
Dept. of Psychiatry
Yale Medical School
2 Church St., Suite 215
New Haven, CT 06519
Tel: 203-785-5306
Fax: 203-737-3591
[log in to unmask]
On Dec 19, 2009, at 10:43 PM, Scott Kolbe wrote:
> some things to consider.
> if you perform any realignment steps on your data (including eddy-
> current correction which is the usual first step) the data will be
> smoothed by the image interpolation.
> So TBSS actually leads to more smoothing because of the non-linear
> coregistrations performed on the DT images.
>
> as Matt says, it's worth checking your sequence. you should be
> collecting at least one B0 image for every ~6 DWIs. that will help
> with SNR. I know the standard Siemen's sequence and potentially
> Phillips also don't allow you to collect mulitple B0 images by
> default. You images resemble those from the standard Siemen's
> sequence.
>
> cheers
> s
>
>
>
> Matt Glasser wrote:
>> It depends on what you plan to use the data for. This will create
>> big
>> problems for tractography, but might be acceptable for TBSS or ROI
>> based FA
>> analyses. You will need to keep in mind that smoothing like this
>> will
>> increase partial volume effects significantly. It is partly for
>> this reason
>> that TBSS was developed, as smoothing has unpredictable effects on
>> what is
>> found to be significant in VBM based analyses of FA data (where
>> smoothing is
>> absolutely required), see Smith et al 2006 in Neuroimage for more
>> details on
>> this issue.
>>
>> If it is still possible to improve your acquisition methods, it is
>> worth
>> revisiting why you are getting this much noise in your FA images,
>> as there
>> might be ways to fix this problem.
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf
>> Of Jiansong Xu
>> Sent: Saturday, December 19, 2009 12:02 PM
>> To: [log in to unmask]
>> Subject: [FSL] DTI: smooth or not smooth
>>
>> Dear All:
>>
>> I would like to know if it is a good idea to smooth DTI raw images
>> before creating FA and other maps.
>>
>> The first attached FA map was created without smoothing the raw
>> images and it is very "noisy". The second attached FA map was
>> created after smoothing the raw images by using: fslmaths input -s
>> 3 output. Relative to the first FA map, the second map appears
>> much more "smooth".
>>
>
> --
> ========================
> Scott Kolbe
> Neuroimaging Group
> Florey Neuroscience Institutes and
> Centre for Neuroscience
> University of Melbourne
> VIC, Australia, 3010.
>
> ph: +61 3 8344 1929
> email: [log in to unmask]
> website: www.neuroimaging.org.au/index.php?id=383
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