Hi,
You would not normally BET the full DTI data in this way. You should
normally BET the nodif_brain_mask (see FDT and TBSS manuals) and then
dtifit uses this mask.
Steve.
On 10 Mar 2009, at 10:12, Siew-Min Gan wrote:
> Hi Steve,
> yeah, I think its unusual too! I think I may have come up with
> some "solutions" but not sure if and why it may work.
>
> The dicom DTI data (30 dir,5 B0) is coverted to ANALYZE and then to
> NIFTI
> I then merge the 35 nifti files into a 4D vol file.
>
> These are the procedures I did where the output FA map has 0
> intensity:
>
> i. Eddycorrect the 4D vol DTI file (output data.nii.gz)
> ii. BET the data.nii.gz file ( using standard brain extraction)
> (output
> nodif_brain_mask)
> iii. DTIFIT in the directory containing (data.nii.gz with skull on),
> nodif_brain_mask, bvecs and bvals)
>
> I made some changes to the method above which seemed to derive FA maps
> with no 0 intensity voxels. However, the FA values differ in each
> voxels
> from the two methods I tried.
> Please let me know which way you think may work better.
>
> If I repeat the above steps in order, but when running bet, I choose
> "Apply to 4D FMRI data" with -F -f 0.2 -g 0 instead of "running bet
> using
> standard brain extraction" with -f 0.5 -g 0, the output FA maps from
> DTIFIT do not have 0 intensity voxels.
> Alternatively, if I do BET as step i with -F -f 0.2 -g 0, and then
> eddycorrect the 4D deskulled dti brain output from BET, the output
> FA maps
> also do not have 0 intensity voxels.
>
> The FA values are different in the FA maps derived from the 3
> different ways.
> i) The 1st FA map from eddycorrect_thenbet_DTIFIT procedure has very
> little white rim, but has 0 intensity voxels in brain white matter
>
> ii) The FA map from eddycorrect_thenbet(-F)_DTIFIT has no 0 intensity
> voxels, but a denser white rim voxels as well as brain white matter
> voxels
> with intensity values > 1. These brain matter voxels with intensity >1
> coincides with the 0 intensity voxels in the 1st FA map voxels above.
>
> iii) The FA maps from bet(-F)_theneddycorrect_DTIFIT has no 0
> intensity
> voxels, it has a dense white rim voxels but much less brain white
> matter
> voxels with intensity values >1.
> White matter Voxels with 0 intensity on the 1st FA map or intensity
> >1 on
> the 2nd FA map above, would have a FA values of between 0 and 1 in
> the 3rd
> FA map. White matter Voxels with intensity>1 on the first two FA
> maps (i.e
> 1.03) would have an FA values of 0.33 on this FA map. For most
> voxels of
> 0<intensity<1, the FA values in the 1st and 2nd FA map are identical
> but
> it is lower in the 3rd FA map.
>
> May I ask if the registration in eddycorrect on deskulled brain (i.e
> output from BET) works better than on brain_with skull on? I'm also
> curious why would the FA values in the FA maps output be different
> in the
> 3 above methods, in terms of voxels with 0 intensity corresponding to
> those >1, and the absolute values between the 2nd and 3rd FA maps.
>
> This would help me decide whether to use the 2nd or 3rd method to
> process
> the data.
>
> Many thanks, and apologies for the long email!
>
> Siewmin
>
>
>
>
>
> You mean you're getting zeroes in the FA output from dtifit _before_
>> any further processing (e.g. from BET or tbss_1_preproc) ? I think
>> this would be unusual and you should carefully check the data that
>> was
>> input to dtifit.
>>
>>
>>
>>
>> On 8 Mar 2009, at 05:42, Siewmin Gan wrote:
>>
>>> Hi all,
>>> I've noticed some pixels with 0 intensities in the white
>>> matter of my FA map output
>>> from DTIFIT, and bloches around the white matter regions (with 0
>>> intensities) in the all_FA
>>> map from tbss_3_postreg -S output. These occur near the pixels/
>>> regions around the
>>> temporal stem white matter.
>>> I've checked my bvals, and bvecs (30 directions) which looks ok,and
>>> would like to ask if it's
>>> "normal" to have some pixels with 0 intensities in FA maps?
>>> However, the bloches of 0 intensity in the all_FA map in tbss are
>>> almost 10-15 pixels big.
>>> Because they occur around the white matter, some bits of the FA
>>> skeleton passing by the
>>> temporal stem is broken up. I'm not sure why this problem exist.
>>>
>>> Much appreciated for some kind advice.
>>>
>>> Thanks.
>>>
>>> Siewmin
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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