[Insight-users] Re: (HOW TO GETDATA)
Luis Ibanez
ibanez at choroid.cs.unc.edu
Mon Jan 7 13:04:33 EST 2002
Lydia,
The process that you describe looks Ok.
Are the two files (header and raw data)
in the same directory ?
The only suspicious thing I can see is
to create the header file with MSDEV.
[ There is nothing like Vim :-) ]
Could you please post to the list:
1) the header file that you created
attached to an email.
2) the EXACT size of the binary data file
that you got from the BrainWeb
(after decompression).
It could be a mismatch between the header and
the raw data file.
Luis
=======================================
On Mon, 7 Jan 2002, lydia ycl wrote:
> Hi Luis and insight users!
> Sorry to bother you again but I still have the
> message "problems in reading file format"
> That's wha I did
>
> 1.I dowlowded the file and named it brainweb from the site
>
> 2.I renamed it as .gz (under msdos) and unzipped it with
> Gunzip
>
> 3.I got a file whose size was nearly 6MB
>
> 4.I renamed this file as a raw file
>
> 5. I created from the MSDEV a text file (brain.mhd)
>
> 6.I put on it the information concerning the pixel size and
> thickness:
> 181,217,181
> MET_UCHAR
> 1.0 1.0 1.0
> False
> brainweb.raw
> I got this information from the site of course
>
> 7.I run the Gaussian filter project
>
> 8. I opened the file "brain.mhd"
>
> 9. The result is the message "problems in ......file format"
>
> Is there any mistake in what I did?
>
> Thanks again to reply and sorry for the disturbs
>
> Regards
>
> Lydia
>
> > -------Message d'origine-------
> > De : Luis Ibanez <ibanez at choroid.cs.unc.edu>
> > Date : 07/01/2002 16:10:30
> >
> >
> > Hi Lydia,
> >
> > The file that you get from the BrainWeb is named
> > "brainwe1" with no extension.
> >
> > You might want to change its extension to ".gz" in
> > order to make gunzip recognize the file as a compressed
> > file.
> >
> > Once decompressed, you should find only one file
> > which is the raw binary data for the image. The file,
> > again is lacking any extension. We use to rename it
> > and put the extension ".raw", but this is purely a
> > convention.
> >
> > The information concerning the size in pixels and the
> > resolution in milimeters of the image was displayed
> > in the second page of the BrainWeb download sequence.
> > You will need this information for writing the MetaImage
> > header file.
> >
> >
> > Hope that helps.
> >
> > Luis
> >
> > ======================================
> >
> > On Sun, 6 Jan 2002, lydia ycl wrote:
> >
> > > Dear Luis,
> > > I followed all the instructions but I foud a problem in
> > > decompression with GUNZIP and even with Winzip
> > > for /compression option) for Windows platform
> > > Do you get after decompression 2 files? what are the
> > > extensions?
> > > Sorry for bothering you again.
> > > Regards
> > > Lydia
> > >
> > > > -------Message d'origine-------
> > > > De : Luis Ibanez
> > > > Date : 04/01/2002 19:53:32
> > > >
> > > >
> > > > Hi Lydia,
> > > >
> > > >
> > > > On Fri, 4 Jan 2002, lydia ycl wrote:
> > > > > it's a pity for the operating room project.
> > > >
> > > > ???
> > > > Did you have further problems after updating your ITK
> > > checkout ?
> > > >
> > > >
> > > >
> > > >
> > > > > For the Gaussian filter project, I couldn't find
> which
> > > > > image format should I use. I tried many of them but
> each
> > > > > time it failed in reading the file. May I ask you to
> > > give
> > > > > me the right format (even pgm didn't work)
> > > >
> > > >
> > > > The format that GaussianFilter is accepting
> > > is "MetaImage".
> > > > Here is how you can create one image in the appropiate
> > > format.
> > > >
> > > > Metaimages are composed of a Header file and a Raw
> data
> > > file.
> > > > You can get raw data from the BrainWeb project and
> write
> > > the
> > > > corresponding MetaImage header for it.
> > > >
> > > > Do the following:
> > > >
> > > > 1) In order to get RAW data, go to :
> > > >
> > > >
> > >
> http://www.bic.mni.mcgill.ca/brainweb/selection_normal.html
> > > >
> > > > - Select the Image modality you prefer : T1, T2, PD
> > > > - Select "Slice Thickness" = 1mm
> > > > - Select "Noise" = 3
> > > > - Select "non-uniformity" = 20
> > > >
> > > > then click in Download.
> > > > That will prompt you to another web page where you
> have
> > > > a header file (which is different from the MetaImage
> > > header),
> > > > and a new set of selections:
> > > >
> > > > - Select "File format" = raw byte (this is very
> > > important)
> > > > - Select "Compression" = gunzip (you'll get a .gz
> file)
> > > >
> > > > and fill out your name, institution and e-mail
> > > > this will help them to get funding for continuing
> > > > with their project. :-)
> > > >
> > > > Then, click on "Start download"
> > > >
> > > > you will be prompted to provide a file name for the
> data.
> > > >
> > > > Then, sit back, relax and take your coffee while the
> > > > about 5Mb got copied into your machine.
> > > >
> > > > When you are done with the download, decompress the
> > > > file with "gunzip". You should get a text header and
> > > > a raw data file.
> > > >
> > > >
> > > > 2) In order to create the MetaImage header, cut paste
> > > > the following lines in a "new" file with extension
> > > > ".mhd".
> > > >
> > > >
> > > > NDims = 3
> > > > DimSize = 181 217 180
> > > > ElementType = MET_UCHAR
> > > > ElementSpacing = 1.0 1.0 1.0
> > > > ElementByteOrderMSB = False
> > > > ElementDataFile = brainweb165a10f17.raw
> > > >
> > > >
> > > >
> > > > Now,
> > > > replace the values in front of DimSize for the image
> size
> > > > that is indicated in the text header file that you
> > > > got from BrainWeb. You should use the values indicated
> > > > under the "length" column as : ( xspace, yspace,
> zspace).
> > > >
> > > > Keep the MET_UCHAR because you selected "raw byte
> > > > (unsigned)" at BrainWeb.
> > > >
> > > > Change the "ElementDataFile" = "brainweb...." for
> > > > the name of the raw data file that you just downloaded
> > > > from the BrainWeb project.
> > > >
> > > >
> > > >
> > > > 3) That's it !
> > > >
> > > >
> > > >
> > > > Now you should be able to load this file from the
> > > > GaussianFilter program. Select "File->Open" from
> > > > the bar menu, and look for the ".mhd" header file.
> > > >
> > > > Make sure that the raw data file and the header file
> > > > are in the same directory.
> > > >
> > > >
> > > > Take into account that the load will take a couple
> > > > of seconds because the file is about 5Mb.
> > > >
> > > > You might want also to check the amount of RAM memory
> > > > in your machine to make sure that it can handle all
> > > > the intermediary images.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Please let us know if you encounter any dificulties
> > > > creating this data file.
> > > >
> > > >
> > > >
> > > > Thanks
> > > >
> > > >
> > > > Luis
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Insight-users mailing list
> > > > Insight-users at public.kitware.com
> > > > http://public.kitware.com/mailman/listinfo/insight-
> users
> > > >
> > > >
> > >
> _________________________________________________________
> > > Le journal des abonnés Caramail -
> http://www.carazine.com
> > >
> > >
> >
> > --
> > Luis Ibanez CB#:
> 7060
> > Research Assistan Professor phone:
> (919) 843 5436
> > Division of Neurosurgery fax:
> (919) 966 6627
> > University of North Carolina at Chapel Hill email:
> ibanez at cs.unc.edu
> > Chapel Hill, NC 27599-7060
> http://www.cs.unc.edu/~ibanez
> >
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at public.kitware.com
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
> >
> _________________________________________________________
> Le journal des abonnés Caramail - http://www.carazine.com
>
>
--
Luis Ibanez CB#: 7060
Research Assistan Professor phone: (919) 843 5436
Division of Neurosurgery fax: (919) 966 6627
University of North Carolina at Chapel Hill email: ibanez at cs.unc.edu
Chapel Hill, NC 27599-7060 http://www.cs.unc.edu/~ibanez
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