[Mrtrix-discussion] NaN values in response.txt
romain valabregue
romain.valabregue at upmc.fr
Tue Sep 4 01:44:18 PDT 2012
Dear all
Just a short comment about the first point : Using nifti file for DWI
data is very convenient especially when one use other software to do the
dti preprocessing (eddy current correction and epi unwarping). Waiting
for the next mrtrix version (where it may be available ?) I use fsl to
do the dti preprocessing and I wrote a small matlab code that take the
4D nifti DTI volume with bval and bvecs and on the gradient table in
mrtrix format (and I apply the rotation of the nifti file to the bvec)
cheers
Romain
Le 28/08/2012 04:25, Donald Tournier a écrit :
> Hi Chris,
>
>
> On a different note: in the process of looking at the data you sent
> over, I had a quick look through your script. There's a few things I'd
> like to mention, which I think others might also want/need to hear.
> Here goes:
>
> *Using NIfTI to store the DWI data:*
> *
> *
> I notice you're supplying a NIfTI image for the DWI, and a separate
> gradient encoding file. While there's nothing wrong with that per se,
> you need to make double-sure that your encoding file is correct /for
> each scan/. MRtrix assumes gradients are in the scanner coordinate
> system (also typically assumed in DICOM data - exception being GE),
> whereas FSL expects assumes they are in the image axes coordinate
> system. These two won't match if the images are acquired in a
> non-axial or oblique plane, and in general won't match between scans
> even if acquired using the same protocol. This rotation needs to be
> accounted for when converting between bvecs/bvals and the MRtrix
> encoding file. I assume you've probably already sorted that out, but
> thought I'd flag this issue again just in case.
>
> I would strongly recommend that everyone convert their data directly
> from the raw DICOM images to .mif (or .mih) format, since the gradient
> information will then be read directly by MRtrix and stored in the
> appropriate format within the image header - no need to supply the
> encoding file separately, which gets rid of a potential source of user
> error.
>
> *Use of -normalise option in csdeconv:*
>
> I strongly advise /against/ the use of the -normalise option of
> estimate_response. Although the response function might be normalised,
> the FODs derived using csdeconv will not be (unless also processed
> using -normalised, but that introduces other issues with CSF
> contamination, as discussed previously in this thread
> <http://www.nitrc.org/pipermail/mrtrix-discussion/2012-July/000472.html>).
> Using a non-normalised response function and non-normalised csdeconv
> actually produces relatively well normalised FODs, since the response
> is then scaled appropriately for the DW signal.
>
> *Use of gen_WM_mask:*
>
> I also strongly advise against the use of gen_WM_mask. It's a bit of a
> Heath Robinson hack job, using fairly arbitrary heuristics to kinda
> identify voxels that ought to correspond to white matter - not really
> based on sound principles. I included it in the original release as I
> thought it would provide a good rough mask of WM to seed from, but
> it's since become clear that it doesn't work all that well, and
> produces variable results depending on the SNR, b-value, and number of
> directions. In hindsight, I shouldn't have included in the release,
> and it won't be available in future major releases.
>
>
> *Creating the mask:*
>
> The command you use creates a mask from a single b=0 image. A more
> robust approach, now recommended in the documentation, is to use the
> average of all volumes in the DWI run - basically improves the SNR:
>
> $ average dwi.mif -axis 3 - | threshold - - | median3D - - | median3D
> - mask.mif
>
>
> *Getting the single-fibre mask:*
>
> This is another command that has changed in recent versions. No big
> deal, but the current recommended command is:
>
> $ erode mask.mif -npass 3 - | mrmult fa.mif - - | threshold - -abs
> 0.7 sf.mif
>
>
>
> That's all I had to say. Just thought I'd take the opportunity to
> clarify a few things...
>
> Cheers,
>
> Donald
>
>
>
> On 27 August 2012 12:18, Donald Tournier <d.tournier at brain.org.au
> <mailto:d.tournier at brain.org.au>> wrote:
>
> Hi Chris,
>
> I can't think of much that could cause this problem, but the most
> obvious one is supplying an empty single-fibre mask at the
> estimate_response step. Another reason might have been if any of
> the single-fibre voxels has one or more zero DW intensities - but
> I've just looked at the code, and there are safeguards in place to
> handle negative or zero DW intensities, so I can't see that it
> could be that either. If none of this helps, maybe you can send me
> one of the offending data sets so I can have look?
>
> Cheers,
>
> Donald.
>
>
> On 27 August 2012 11:57, Chris Adamson <chris.adamson at mcri.edu.au
> <mailto:chris.adamson at mcri.edu.au>> wrote:
>
> Donald,
>
> I am getting NaN values in the response.txt file in rare
> cases. How can
> I diagnose the problem/fix it? What should I look for in the
> data that
> would cause a failure of the ellipse fitting?
>
> Chris.
> --
> Dr Christopher Adamson, PhD (Melb.), B Software Engineering
> (Hons.,
> Monash)
> Research Officer
> Developmental Imaging, Critical Care and Neurosciences
>
> Murdoch Childrens Research Institute
> The Royal Children's Hospital
> Flemington Road Parkville Victoria 3052 Australia
> T 9906 6780
> M XXXX XXX XXX
> E chris.adamson at mcri.edu.au <mailto:chris.adamson at mcri.edu.au>
> www.mcri.edu.au <http://www.mcri.edu.au>
>
> ______________________________________________________________________
> This email has been scanned by the Symantec Email
> Security.cloud service.
> For more information please visit http://www.symanteccloud.com
> ______________________________________________________________________
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> <mailto:Mrtrix-discussion at www.nitrc.org>
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>
>
>
> --
> *Dr Jacques-Donald Tournier
> *
> Research Fellow
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7033
> Fax: +61 3 9035 7307
> www.florey.edu.au <http://www.florey.edu.au>
>
>
>
>
>
> --
> *Dr Jacques-Donald Tournier
> *
> Research Fellow
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7033
> Fax: +61 3 9035 7307
> www.florey.edu.au <http://www.florey.edu.au>
>
>
>
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20120904/e1d1ee7f/attachment-0001.html
More information about the Mrtrix-discussion
mailing list