[SCIFIO] SCIFIO post from phsiao at cs.unc.edu requires approval

[Mark Hiner]

Hi Joe,

 Thanks for reporting this issue.

reader->SetImageIO( io );
>

 Just so you know, this is just disabling SCIFIO I believe, and defaulting
to the ITK DICOM ImageIO.

 Does the output file have the correct number of total planes? If not, you
might try "-d 5" just to test. The dimension order is XYCZT but XYZ are the
dimensions with length more than 1. The SCIFIO plugin is supposed to
account for that but it could be a bug.

 Otherwise if the dimensions are correct it could be an issue with the
dataset being interleaved.

 I'll try to look at it soon.

Thanks,
Mark


From: Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>
> To: scifio at scif.io
> Cc:
> Date: Tue, 15 Oct 2013 14:29:23 -0400
> Subject: Error reading a 32-bit nrrd image via ITK
> I am having trouble using SCIFIO in ITK to read a 32-bit .nrrd image in my
> own program. The attached is a 32-bit 3-dimensional test image.
>
> Then I used the following command to test with the SCIFIO test program:
>
> SCIFIOTestDriver.exe itkSCIFIOImageIOTest sample_5.nrrd 123.ome.tiff -w -d
> 3 -t float
>
> The output '123.ome.tiff' has wrong pixel values and looks wrong in ImageJ.
>
> After I dig deeper, I found that in in 'itkSCIFIOImageIOTest.cxx', if I
> comment out this line
>
>    reader->SetImageIO( io );
>
> to use ITK's default ImageIO, the output image becomes normal.
>
> Thanks,
> Joe
>
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