[Insight-users] Unexplained file extensions in ITK

[Bill Lorensen]

Reuben,

I believe that the Visible Human MR data is stored in a GE Signa or
Genesis format. It's been many years since I looked at that data.

This file: ftp://ftp.nlm.nih.gov/visible/bitmaps/mri/mri.txt describes
the format. It looks as though you could easily make a meta file for
this data. Perhaps an Insight user has already done this.

Bill

On Wed, Apr 9, 2008 at 4:54 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
> Hi Reuben,
>
>
>                    Welcome to ITK !!
>
>
> I'm not aware of any fileformat that uses the extensions:
>
>      ".t1"
>      ".t2"
>      ".pb"
>
> It is tempting to especulate that they simply refer to
> MRI modalites "T1", "T2" and "Proton Density".
>
>
>
> If the files actually contain DICOM files, then you
> should be able to read them directly with the ITK
> ImageFileReader, since the DICOM reader doesn't expect
> any file name extension in particular.
>
> I would suggest you try reading one of the 2D slices
> with the example:
>
>     Insight/Examples/IO/ImageReadWrite.cxx
>
> with a command line similar to:
>
>     ImageReadWrite   input.t1  output.mhd
>
>
> and then visualize the output with
>
>     Slicer (www.slicer.org)
>     ParaView (www.paraview.org)
>
>
> Actually, you may be able to read the .t1, .t2, .pd
> files directly with Slicer, since Slicer uses the
> ITK readers.
>
>
> Also, you could use the Example:
>
>       DicomImageReadPrintTags.cxx
>
> just to check if there are actual DICOM tags in
> these files.
>
>
>
> Please let us know if you find any problem,
>
>
>    Thanks
>
>
>       Luis
>
>
> --------------------
> Reuben Kraft wrote:
> > Hello Luis,
> >
> > I am a new user to ITK. I submitted a request to the users group but have
> not heard anything back,  My background is in finite element modeling and I
> am interested in contributing some features into ITK in the future.  Right
> now, I am trying to get up to speed with my first goal of reading MRI
> information obtained from the Visible Human Project.
> > I received files from a colleague with little description as to what
> format they are in.  They have file extensions *.pd. *.t1, and *.t2.   From
> what I am able to find online, it seems they may be DICOM format, but I am
> not sure.
> > I have not found anything in the insight users forum about reading files
> with this extension, and I have been trying some things on my own with no
> success.  ITK does not recognize this extension and prefers another.  Do I
> need to change the file extension?  If so, to what?  Any suggestions on
> further reading I can do to understand how to get these image slices into
> ITK?
> >
> > A short comment about these file extensions may be useful in the ITK
> user's guide in the future.  Thanks for your time, and sorry for the newbie
> question.
> >
> > Respectfully,
> > Reuben Kraft, Ph.D.
> >
> >
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