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Thanks, reassuring to hear it's a sensible solution. Pulsation is a
possibility, but we seem to consistently see this in the B=0 for
affected scans and not at all in the weighted images (for one of the
protocols we have 7 interspersed b=0, with the subject we looked at
most closely I'd say 6 of those had the same very low b0 with 1 more
borderline). They're also quite focal, I'll see if I'm allowed to post
some screenshots if they'd be useful for other people.<br>
<br>
Philip A Cook wrote:
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cite="mid:45529E4B-CA75-49BA-BBE1-5D19CAB1733A@mail.med.upenn.edu"
type="cite">
<pre wrap="">I was just thinking we needed a tool to test this. Yes, having b=0 measurements less than the DWI is a bad sign. I agree it is unlikely to be genuinely anatomical. Maybe it is due to CSF pulsation? If the boundary of the ventricles moves slightly it could put more CSF into a voxel during some of the DWI measurements. But if you're seeing signs of signal loss away from the boundary, maybe that is the problem.
The masking you suggest sounds like a good way to identify the problem areas.
On Jan 29, 2013, at 11:39 AM, Ian Malone wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
Thanks for getting back to me. We've had a closer look at the images now. The high FA values are typically around the caudate and the rest of the ventricle boundary. This seems to correspond to voxels where the B=0 intensity is LOWER than the weighted intensity in the source images. Obviously that's going to cause problems[1]. I don't think this can be genuinely anatomical or pathological, is there any mechanism where that can ever happen? I'm wondering if it might be an artefact caused by the high-contrast CSF-brain boundary around the ventricles in the B=0 compared to weighted images, but there does seem to be a trail of low B=0 intensity up from the putamen in these images, so hard to be definite.
What we're considering doing is producing a mask image with a per-voxel criteria like mean b0 < mean weighted. Does this sound sensible? RESTORE would hopefully reject these too, but we have quite a lot of data which has already been processed.
[1] They just happen to be more apparent in the non-linear fit. These voxels do have exit code 0. Fitted diffusivity is very low (10^-5 mm^2/s axial, 10^-11 transverse).
Thanks again,
Ian
Philip A Cook wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Ian,
If the nonlinear fit fails to converge, you should get the linear result in the voxel. It sounds like it is converging (exit code 0) but it is converging on a bad solution. I expect that the ADC will be strange as well.
You might have better luck with RESTORE.
Phil
On Jan 28, 2013, at 1:30 PM, Ian Malone wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
We're using Camino on some Siemens data, 42 directions, b=1000 s/mm^2, there are a few different protocols (different sites), but the problem seems to affect a few of them, one has 7 b=0 acquisitions. Fitting tensors using the non-linear least squares fit from modelfit we find a small number of voxels with FA>0.999, mostly in the caudate (sorry, don't have all the details yet on frequency). There are no obvious problems with the raw data and using FSL's FDT to do a simple least squares log signal fit doesn't produce this error. Looking at the error codes there are some 6's (bad data), but not corresponding to the problem voxels. I'd thought it might be a convergence problem, but we don't seem to be getting any error code = 2.
Does anyone have any suggestions for things we could try to solve this problem? The Camino version is a fairly recent release (r1014).
Thanks for your time,
Ian
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