[Camino-users] problem with mbalign.

[Darren Gitelman]

Dear Phil

Yes and yes. There are several b=0 measurements and they are in the scheme
file with the directions and b value = 0.

I did figure out that one problem was that my images were not all big
endian and unfortunately camino doesn't really seem to understand 1 file
nifti files, but I fixed all that and confirmed it by making sure that the
image files had proper values. The mask file also appropriately covers the
brain.

Darren


On Thu, Nov 17, 2011 at 10:09 AM, Philip A Cook
<cookpa at mail.med.upenn.edu>wrote:

> 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
> > _______________________________________________
> > Camino-users mailing list
> > Camino-users at www.nitrc.org
> > http://www.nitrc.org/mailman/listinfo/camino-users
>
>


-- 
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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