<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">Do you have any b=0 measurements in your data? I think the problem is that it's trying to normalize the data by dividing each measurement by the mean b=0 measurement. The non-linear tensor fit only operates on the non-zero b-values. If there is
no b=0, the results might look reasonable in terms of anisotropy, but the scale could be off.</div>
<div class=""><br class="">
</div>
<div class="">If you have a very small minimum b-value (eg, 5 s / mm^2), you could try setting that to 0 in the scheme file. Then it would normalize by those measurements, and the estimated S_0 would be very close to correct.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Jan 18, 2018, at 10:29 AM, Marie Amelie <<a href="mailto:mariamelie.sque@gmail.com" class="">mariamelie.sque@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="">
<div class="">Dear camino users,<br class="">
<br class="">
</div>
I am using camino to fit the tensor model (nonlinear optimization, constrained to be positive semi-definite) on dMRI data with the following command:<br class="">
<br class="">
modelfit -inputfile dwi.Bfloat -schemefile schemefile.scheme -inversion 2 -bgmask mask_Bfloat.nii.gz -maskdatatype float -outputfile dt.Bdouble<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">The process globally seems to work fine: the tensor fitting and then the derived scalar maps (produced as indicated in camino's DTI tutorial) are ok both at the visual inspection and by comparing their values to the ones computed by a previous
tensor fitting with another tool. However in the terminal I am seeing many instances of these warnings:</div>
<div class=""><br class="">
</div>
<div class="">Jan 17, 2018 10:50:35 AM imaging.DW_Scheme normalizeData<br class="">
WARNING: Can't use normalization constant NaN</div>
<div class=""><br class="">
</div>
<div class="">My question is: can you explain me why I am seeing these warnings? Can I trust my tensor fit despite these warnings? Again, scalar maps and their values look globally fine.<br class="">
</div>
<div class="">Could it be related to my brain/backgound mask? It is actually rather conservative (i.e. tends to exclude some voxels of the brain rather than include background voxels), but I can't exclude that in some instances it might also include some background
(even if perhaps not that frequently). <br class="">
</div>
<div class="">I am a new camino user, I apologize in advance if this is a basic question.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">------------------------------<wbr class="">------------------------------<wbr class="">----------------<br class="">
</div>
<div class="">Here follows additional information.</div>
<div class=""><br class="">
</div>
<div class="">Before the tensor fit, I performed an eddy-current correction (MRtrix' dwipreproc) and then did with camino:</div>
<div class="">fsl2scheme -bvecfile bvec_rot.txt -bvalfile bval.txt > schemefile.scheme<br class="">
</div>
<div class="">image2voxel -4dimage dwi.nii.gz -outputfile dwi.Bfloat<br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">For completeness, I report here that I also get some instances of this error:</div>
<div class="">Jan 17, 2018 10:50:32 AM misc.LoggedException logException<br class="">
WARNING: Exception in thread "main" class optimizers.<wbr class="">MarquardtMinimiserException: Singular Matrix in gaussj - 2
<br class="">
at optimizers.MarquardtMinimiser.<wbr class="">gaussj(MarquardtMinimiser.<wbr class="">java:362)<br class="">
at optimizers.MarquardtMinimiser.<wbr class="">mrqmin(MarquardtMinimiser.<wbr class="">java:231)<br class="">
at optimizers.MarquardtMinimiser.<wbr class="">minimise(MarquardtMinimiser.<wbr class="">java:156)<br class="">
at inverters.NonLinearDT_<wbr class="">Inversion.invert(NonLinearDT_<wbr class="">Inversion.java:135)<br class="">
at apps.ModelFit.execute(<wbr class="">ModelFit.java:156)<br class="">
at apps.EntryPoint.main(<wbr class="">EntryPoint.java:290)<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">but from the camino FAQ webpage I think I understood their meaning.</div>
<div class=""><br class="">
</div>
<div class="">I am running it on a Ubuntu 16.04 machine. <br class="">
</div>
<div class="">The git log of my camino version is:<br class="">
</div>
<div class="">commit af55b0acd7895b7d1dafa040df60c4<wbr class="">94369b138a<br class="">
Author: Philip Cook <<a href="mailto:cookpa@mail.med.upenn.edu" target="_blank" class="">cookpa@mail.med.upenn.edu</a>><br class="">
Date: Fri Oct 6 12:00:17 2017 -0400<br class="">
<br class="">
ENH: Allow non-zero unweighted measurements for dtspd<br class="">
<br class="">
------------------------------<wbr class="">------------------------------<wbr class="">---------------<br class="">
</div>
<div class="">Any help on my question is highly appreciated.</div>
<div class="">Thank you in advance.</div>
<div class=""><br class="">
<br class="">
</div>
</div>
_______________________________________________<br class="">
Camino-users mailing list<br class="">
<a href="mailto:Camino-users@www.nitrc.org" class="">Camino-users@www.nitrc.org</a><br class="">
https://www.nitrc.org/mailman/listinfo/camino-users<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>