Hi,
Indeed, the projection should be working fine. If you're _sure_ that
the MD conversion to the right format with tbss_1_preproc was fine
then it's not clear to me why the null test is giving a signal - it's
probably worth you uploading the entire directory to us to have a
quick look. (btw, for other reasons I was putting simulated null data
into the TBSS skeleton recently and indeed the expected null results
came out perfectly.)
Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then email me the upload ID.
Cheers, Steve.
On 28 Oct 2006, at 21:39, Win Gongvatana wrote:
> Hi Steve,
>
> Thank you very much for the clarification. So it seems I can rule
> out the MD
> projection issue as a source of our problematic statistical results
> (i.e.,
> the significant group differences in most voxels even with the null
> validation data set). Do you have some ideas about other potential
> sources
> of problem? The same design matrices for randomise were used for
> the MD
> analyses as the FA analyses; and the latter yielded results
> consistent with
> expectation.
>
> Win
>
> On Sat, 28 Oct 2006 08:13:22 +0100, Steve Smith
> <[log in to unmask]> wrote:
>
>> Hi - if you are following the tbss_non_FA script and section in the
>> manual, the projection vectors themselves are _still_ being estimated
>> from the FA data - we know that this marks the tracts out well, with
>> highest values at the tract centres, and then these projection
>> vectors are being used to decide which voxels to take the MD value
>> from to put onto the skeleton. Hence for MD you won't necessarily get
>> a simple relationship between the source and destination values, but
>> you should be achieving the goal of taking the MD from the tract
>> centres (as defined by the FA) to put onto the skeleton.
>>
>> I hope this clarifies this? Cheers, Steve.
>>
>>
>>
>> On 28 Oct 2006, at 00:56, Win Gongvatana wrote:
>>
>>> Hi Steve,
>>>
>>> Thank you for your reply. I examined the values by overlaying (in
>>> afni)
>>> "all_MD_skeletonized" on "all_MD", and comparing the overlay and
>>> underlay
>>> MD
>>> values of the same subject at each pixel on the skeleton. My
>>> understandin
>>> g
>>> is that the pixel values on the skeleton in "all_MD_skeletonized"
>>> are
>>> derived from searching perpenticularly from the original skeleton
>>> for the
>>>
>>> maximum value, representing the center of the track. These should
>>> therefo
>>> re
>>> be >= the same pixels on "all_MD", which represent the values
>>> before th
>>> e
>>> projection. Our FA data are consistent with this, although MD are
>>> not. Do
>>> es
>>> this sound like I have an incorrect understanding of the process
>>> somehow?
>>>
>>> Thank you in advance for your valueble time.
>>>
>>> Win
>>>
>>> On Fri, 27 Oct 2006 09:03:23 +0100, Steve Smith
>>> <[log in to unmask]> wr
>>> ote:
>>>
>>>> Hi Win,
>>>>
>>>> It sounds like something's very wrong - in particular any null
>>>> validation of the permutation testing should definitely give the
>>>> right results. How does the all_MD (the 4D nonlinear aligned data)
>>>> look - view as a movie loop in FSLView ?
>>>>
>>>> How are you judging whether values go up or down after projection?
>>>> The projected values stay exactly the same (there's no
>>>> interpolation
>>>> involved) so I'm not sure what measure you're using.
>>>>
>>>> Cheers, Steve.
>>>>
>>>>
>>>> On 26 Oct 2006, at 21:16, Win Gongvatana wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I was wondering what has been your experiences with tbss and mean
>>>>> diffusivity (or other non-FA) data. We've successfully used
>>>>> tbss on
>>>>> the F
>>>>> A
>>>>> data in our lab, but still have some trouble with MD. The
>>>>> recommended ste
>>>>> ps
>>>>> were followed through to tbss_non_FA to get the projected MD
>>>>> skeletons fo
>>>>> r
>>>>> individual subjects (based on the original FA skeleton, as
>>>>> recommended).
>>>>> Performing t-tests on our various data sets processed with this
>>>>> technique
>>>>> ,
>>>>> "randomise" yielded wildly significant group differences (1-alpha
>>>>>> .99 f
>>>>> or
>>>>> the majority of voxels) even with our "control vs. control"
>>>>> analyses.
>>>>>
>>>>> One thing that I find unusual is that the projected MD values
>>>>> on the
>>>>> skeleton are sometimes lower than the values before projection,
>>>>> which is
>>>>> counter-intuitive to my understanding of the "perpendicular
>>>>> search"
>>>>> strat
>>>>> egy
>>>>> for the projection. Inspecting the projected FA values shows them
>>>>> to alwa
>>>>> ys
>>>>> be >= the values before projection.
>>>>>
>>>>> If this matters, my scaling factor for MD at step 1 was 2000 (our
>>>>> values
>>>>> range from about 0 to 5, with no negatives).
>>>>>
>>>>> Any advice/suggestions would be greatly appreciated.
>>>>>
>>>>> I'd also like to thank the FSL/TBSS team for the incredibly useful
>>>>> tools
>>>>> you
>>>>> made available.
>>>>>
>>>>> Win
>>>>
>>>>
>>>> -------------------------------------------------------------------
>>>> --
>>>> ---
>>>
>>>> ---
>>>> 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
>> ---------------------------------------------------------------------
>> ---
>> ---
>> =====================================================================
>> ====
------------------------------------------------------------------------
---
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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