Hi Laura/Saad,
indeed, it is a calculated trace-weighted image. But I wonder if setting
bvals=1000 (or whatever you use) and bvecs=0,0,0 , which is contradictory,
would not result in skipping the volume from the calculation. Isn't there
such kind of mechanism to skip the volume implemented in FSL. It could be
useful and faster that fslplit, fslmerge.
Best,
Martin
On Thursday 28 August 2008 18:13:59 Saad Jbabdi wrote:
> Hi Laura,
>
> Isn't the last volume simply the mean diffusivity image (or the trace
> of the tensor)?
> In this case you don't want to include it in the data, so you may
> remove it (using fslroi), and also remove the last element in your
> bvals file, and the last line (or column) of your bvecs file, then run
> dtifit and bedpostx again.
>
> Cheers,
> Saad.
>
> On 28 Aug 2008, at 14:39, Laura Danielian wrote:
> > I'm collecting my DTI data on a Philips 3T with the following
> > gradient table (see below).
> > To obtain proper vectors, the x-direction needs to be inverted.
> > However, I'm not sure
> > how to handle the final direction in the table (33: 100,100,100).
> > According to Philips, this
> > is "fake" data and can be ignored-thus I assumed it wouldn't play a
> > role in the tensor
> > calculation. However, I've run BEDPOST with this value positive and
> > negative (with all
> > other x-direction gradient values inverted) and I get different
> > results.
> >
> > I then ran BEDPOST with the gradients un-inverted and used fslmaths
> > to invert the th and
> > ph merged_samples files and reran make_dyadic_vectors. The results
> > were close to both
> > previous BEDPOST results with the inverted x-direction (with
> > positive 100 and negative
> > 100 values) but not an exact match for either one.
> >
> > Do you have any advice for how to format this data for the bvecs
> > file? Does it need to be
> > normalized as well?
> >
> > Thanks in advance for your help!
> > -Laura
> >
> > 0: 1.000, 0.000, 0.000
> > 1: 0.000, 1.000, 0.000
> > 2: 0.000, 0.000, 1.000
> > 3: -0.042, -0.115, -0.993
> > 4: 0.1575, -0.201, -0.964
> > 5: 0.232, -0.163, -0.959
> > 6: 0.368, 0.026, -0.930
> > 7: 0.190, 0.374, -0.908
> > 8: -0.117, 0.833, -0.540
> > 9: -0.200, 0.253, -0.947
> > 10: -0.496, 0.134, -0.858
> > 11: -0.014, -0.628, -0.778
> > 12: -0.744, -0.148, -0.651
> > 13: -0.761, 0.320, -0.564
> > 14: -0.181, 0.925, -0.335
> > 15: -0.680, -0.422, -0.600
> > 16: 0.777, 0.471, -0.418
> > 17: 0.924, -0.104, -0.368
> > 18: 0.468, -0.767, -0.438
> > 19: 0.882, -0.189, -0.432
> > 20: 0.690, 0.706, -0.157
> > 21: 0.239, 0.757, -0.608
> > 22: -0.058, 0.984, 0.170
> > 23: -0.537, 0.836, -0.113
> > 24: -0.992, -0.121, -0.042
> > 25: -0.997, 0.071, -0.038
> > 26: -0.872, 0.478, -0.101
> > 27: -0.249, 0.934, 0.258
> > 28: 0.118, 0.992, -0.047
> > 29: 0.338, 0.841, 0.422
> > 30: 0.529, 0.841, 0.116
> > 31: 0.997, 0.055, -0.057
> > 32: 0, 0, 0
> > 33: 100, 100, 100
>
> ---------------------------------------------------------------------------
> Saad Jbabdi,
> Postdoctoral Research Assistant,
> Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222545 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad
> ---------------------------------------------------------------------------
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