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
> ---------------------------------------------------------------------------
>
