[Camino-users] problem with mbalign.

[Philip A Cook]

Hi,

Does your data include b=0 measurements? Also, is your mask including non-brain regions? These kinds of errors are common if you include background voxels. 

BTW, if you supply a mask, the -bgthresh option is ignored.


Phil

On Nov 15, 2011, at 7:27 PM, Darren Gitelman wrote:

> Hi
> 
> I am trying to use camino to analyze my DTI data. 
> 
> I am first doing eddy current correction.
> 
> This is my command line:
> 
> [drg at zonda camino]$ mbalign -datatype float -schemefile 36dwi_b1000_bvector.scheme -components 36 -datadims 260 260 65 -voxeldims .73846 .73846 2.0 -sigma 14 -inputfile dti001_ser7.Bfloat -bgmask dti001_mask.nii -eddy -outputfile dti001_ser7_eddy.Bfloat -slicecheck /data/zonda1/pddti/dti001/camino/slicecheck/dti001_slicecheck -bgthresh 20 
> 
> This gives me some initial output:
> 
> :-) I have everything I need!
> 36 components inside inputfile.
> No temp directory specified. Trying to use /tmp/dti001_ser7_15.11.11_181736.
> Successfully created /tmp/dti001_ser7_15.11.11_181736.
> Linux system detected.
> Disk space temporarily used during calculation is about 5694624000. Make sure space is available!
> Fitting Tensors...
> mask input
> 
> After this I get a lot of output that looks like the following. I get this output whether or not I specify a bgthresh and at a variety of sigma values. Is this to be expected or do I need to fix something?
> 
> Nov 15, 2011 6:17:42 PM imaging.DW_Scheme normalizeData
> WARNING: Can't use normalization constant 0.0
> Nov 15, 2011 6:17:42 PM inverters.RestoreDT_Inversion invert
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2  Fitting failed.  Outputting best DT found, which may be affected by outliers.
> Nov 15, 2011 6:17:43 PM imaging.DW_Scheme normalizeData
> WARNING: Can't use normalization constant 0.0
> Nov 15, 2011 6:17:43 PM inverters.RestoreDT_Inversion invert
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2  Fitting failed.  Outputting best DT found, which may be affected by outliers.
> Nov 15, 2011 6:17:45 PM imaging.DW_Scheme normalizeData
> WARNING: Can't use normalization constant 0.0
> Nov 15, 2011 6:17:45 PM inverters.RestoreDT_Inversion invert
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2  Fitting failed.  Outputting best DT found, which may be affected by outliers.
> Nov 15, 2011 6:17:47 PM imaging.DW_Scheme normalizeData
> WARNING: Can't use normalization constant 0.0
> Nov 15, 2011 6:17:47 PM inverters.RestoreDT_Inversion invert
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2  Fitting failed.  Outputting best DT found, which may be affected by outliers.
> Nov 15, 2011 6:17:57 PM inverters.RestoreDT_Inversion invert
> INFO: Maximum iterations reached without convergence. Final tensor:
>         1.2312659747573168E-9 -1.0053586166159994E-10 -1.4422426735710772E-11
> -1.0053586166159994E-10 1.0873050187771824E-9 2.6988536554535517E-11
> -1.4422426735710772E-11 2.6988536554535517E-11 9.300247616640151E-10
> 
> -- 
> Darren 
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