Thanks Matt,
Yes - I presume you mean the TBSS-derived nonlinear warp fields, which
certainly will help. Note though that the final "alignment" stage in
TBSS (the tract-centre to skeleton projection) would not be easily
usable in this context, and so my concern would still stand to some
extent.
Cheers, Steve.
On 10 Feb 2008, at 15:38, Matt Glasser wrote:
> In the past, I have applied the registration matrices generated by
> TBSS to
> align tractography results before averaging them. You also might
> consider
> this approach to improve tract alignment.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Steve Smith
> Sent: Sunday, February 10, 2008 10:24 AM
> To: [log in to unmask]
> Subject: Re: [FSL] t-test for tractography
>
> Hi - I guess you're feeding in the fdt_paths image from each subject
> into a group-wise t-test? There are various dangers here.
>
> The obvious one is that you will not have very good alignment between
> subjects for such a voxelwise test. This is the primary issue that
> TBSS attempts to resolve. However, if you accept this danger (and,
> maybe smooth a lot......), you can run the voxelwise t-test on the
> tractography output....
>
> Which brings you to a second danger, which is that it will be hard to
> correct for multiple comparisons across space, as the spatial
> autocorrelation structure will be high and complex. However, you can
> probably get over that by using randomise correctly.
>
> I'm sure that Tim/Saad may have further caveats with this....
>
> Cheers, Steve.
>
>
>
>
> On 7 Feb 2008, at 21:06, Paul Geha wrote:
>
>> Dear FSL users,
>>
>>
>> I am running proabilistic tractography (using a mask identified from
>> TBSS)
>> on a group of patients and age matched controls. Is it
>> statisitcally sound
>> to do an unpaired t-test between the 2 groups on the tracts maps
>> obtained ?
>>
>> thanks
>> Paul
>>
>>
>>
>> Paul Geha M.D.
>> Northwestern University
>> The Feinberg School of Medicine
>> Department of Physiology M211
>> 303 E. Chicago Ave.
>> Chicago, IL 60611
>> Tel:312-503 2886
>> Fax: 312-503-5101
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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