If the FA has been transformed but the MD hasn't, they will not be
aligned to each other, so you can't just feed the MD into the TBSS
scripts, regardless of whether the image matrix size is still the same
or not. You would need to apply the same pre-TBSS matrix to the MD
first.
However, also, in general we would not recommend applying any
transformations to the FA (which I think you've done) before running
TBSS, as this will lose some resolution due to the resampling, (unless
you needed to do this for reasons of custom registration processing to
solve difficult registrations in TBSS for example).
Cheers.
On 9 Oct 2008, at 13:41, Hedok Lee wrote:
> Hi Steve,
>
> The reason for having different header information is that I
> coregistered FA image with anatomical while MD image was kept
> unprocessed. I assume it's ok to apply normalization parameters as
> long as two images have the same "space" as in same voxel counts.
> Both images are acquired from the same run.
>
> "FA"
> dim0 3
> dim1 256
> dim2 256
> dim3 26
> dim4 1
> dim5 1
> dim6 1
> dim7 1
>
> "MD"
> dim0 3
> dim1 256
> dim2 256
> dim3 26
> dim4 1
> dim5 1
> dim6 1
> dim7 1
>
>
> Hedok
>
>
> Steve Smith wrote:
>> Hi - if the raw data is in the same space in FA and MD images then
>> this should be fine - however, I would be concerned possibly about
>> why they have different headers though - dtifit should have given
>> all its outputs the same headers, spatially....
>>
>> Cheers.
>>
>>
>> On 9 Oct 2008, at 04:08, Hedok Lee wrote:
>>
>>> Dear FSLers:
>>>
>>> I have a question regarding TBSS normalization of non-FA images. My
>>> apologies if it has been answered already.
>>>
>>> I'm using FSL 4.1 (TBSS with FNIRT).
>>>
>>> Question:
>>> Is it necessary for non-FA to have the same voxel-to-world mapping
>>> as the FA
>>> if I were to analyze the non-FA image using the normalization
>>> parameters
>>> derived from FA?
>>>
>>> For example, a FA image has a nifiti header of
>>>
>>> qto_xyz:1 -1.014429 -0.047513 0.069794 133.319595
>>> qto_xyz:2 -0.048589 1.010437 -0.444181 -129.897827
>>> qto_xyz:3 0.009884 0.090794 4.979743 -71.412193
>>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>>>
>>> But non-FA image (MD) has
>>> qto_xyz:1 -1.015640 0.000000 -0.000000 129.492004
>>> qto_xyz:2 0.000000 1.005132 -0.716720 -128.102585
>>> qto_xyz:3 0.000000 0.145583 4.948366 -78.129471
>>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>>>
>>> I also appreciate if there is a simple way to copy header
>>> information from
>>> FA to non-FA.
>>>
>>> Thanks,
>>>
>>> Hedok
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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