[Insight-users] Re: (HOW TO GETDATA)

[Luis Ibanez]

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 <ibanez at choroid.cs.unc.edu>
> > 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