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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 ---------------------------------------------------------------------------