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

Mon Jan 7 18:51:18 EST 2002

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
> 
> 
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> 
_________________________________________________________
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