[Mrtrix-discussion] NaN values in response.txt

Tue Sep 4 03:32:53 PDT 2012

Hi Romain,

This script sounds like it might be useful for other too. Any chance you
could share it...?

Cheers,

Donald

On 4 September 2012 18:44, romain valabregue <romain.valabregue at upmc.fr>wrote:

>  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> 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> 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
>>> www.mcri.edu.au
>>>
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>>
>>
>>
>>   --
>> *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
>>
>>
>>
>
>
>  --
> *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
>
>
>
>
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-- 
*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
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