Dear Phil<br><br>Yes and yes. There are several b=0 measurements and they are in the scheme file with the directions and b value = 0. <br><br>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.<br>
<br>Darren<br><br><br><div class="gmail_quote">On Thu, Nov 17, 2011 at 10:09 AM, Philip A Cook <span dir="ltr"><<a href="mailto:cookpa@mail.med.upenn.edu">cookpa@mail.med.upenn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<br>
<br>
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.<br>
<br>
BTW, if you supply a mask, the -bgthresh option is ignored.<br>
<br>
<br>
Phil<br>
<br>
On Nov 15, 2011, at 7:27 PM, Darren Gitelman wrote:<br>
<br>
> Hi<br>
><br>
> I am trying to use camino to analyze my DTI data.<br>
><br>
> I am first doing eddy current correction.<br>
><br>
> This is my command line:<br>
><br>
> [drg@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<br>
><br>
> This gives me some initial output:<br>
><br>
> :-) I have everything I need!<br>
> 36 components inside inputfile.<br>
> No temp directory specified. Trying to use /tmp/dti001_ser7_15.11.11_181736.<br>
> Successfully created /tmp/dti001_ser7_15.11.11_181736.<br>
> Linux system detected.<br>
> Disk space temporarily used during calculation is about 5694624000. Make sure space is available!<br>
> Fitting Tensors...<br>
> mask input<br>
><br>
> 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?<br>
><br>
> Nov 15, 2011 6:17:42 PM imaging.DW_Scheme normalizeData<br>
> WARNING: Can't use normalization constant 0.0<br>
> Nov 15, 2011 6:17:42 PM inverters.RestoreDT_Inversion invert<br>
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2 Fitting failed. Outputting best DT found, which may be affected by outliers.<br>
> Nov 15, 2011 6:17:43 PM imaging.DW_Scheme normalizeData<br>
> WARNING: Can't use normalization constant 0.0<br>
> Nov 15, 2011 6:17:43 PM inverters.RestoreDT_Inversion invert<br>
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2 Fitting failed. Outputting best DT found, which may be affected by outliers.<br>
> Nov 15, 2011 6:17:45 PM imaging.DW_Scheme normalizeData<br>
> WARNING: Can't use normalization constant 0.0<br>
> Nov 15, 2011 6:17:45 PM inverters.RestoreDT_Inversion invert<br>
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2 Fitting failed. Outputting best DT found, which may be affected by outliers.<br>
> Nov 15, 2011 6:17:47 PM imaging.DW_Scheme normalizeData<br>
> WARNING: Can't use normalization constant 0.0<br>
> Nov 15, 2011 6:17:47 PM inverters.RestoreDT_Inversion invert<br>
> INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2 Fitting failed. Outputting best DT found, which may be affected by outliers.<br>
> Nov 15, 2011 6:17:57 PM inverters.RestoreDT_Inversion invert<br>
> INFO: Maximum iterations reached without convergence. Final tensor:<br>
> 1.2312659747573168E-9 -1.0053586166159994E-10 -1.4422426735710772E-11<br>
> -1.0053586166159994E-10 1.0873050187771824E-9 2.6988536554535517E-11<br>
> -1.4422426735710772E-11 2.6988536554535517E-11 9.300247616640151E-10<br>
><br>
> --<br>
> Darren<br>
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<br>
</blockquote></div><br><br clear="all"><br>-- <br>Darren Gitelman, MD<br>Northwestern University<br>710 N. Lake Shore Dr.<br>Abbott 11th Floor<br>Chicago, IL 60611<br>Ph: (312) 908-8614<br>Fax: (312) 908-5073<br><br><br>