[Insight-users] Re[1]OperatingRoom and itkFstream.h (HOW TO GET DATA)

[Luis Ibanez]

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