[Insight-users] MultiResMIRegistration

[Luis Ibanez]

HI Christos,

The exception message that you get means that
the fileformat of your image has not been
recognized by any of the existing ITK ImageIO
objects.

In fact, the extension ".raws" will not be
recognized by any of the current ImageIO
objects in ITK.

I assume that those are "raw" files. RAW formats
are *bad*, they are ambiguous and therefore
dangerous as a support for medical images.

The best thing you can do for them is to create
a MetaImage header that points to the raw file
and provides the necessary information concerning
the image dimension, number of pixels, interpixel
spacing, image origin in physical coordinates.

You  can create this header by following the dialog
of the application:

      InsightApplications/MetaImageImporter

or by reading the description of a meta image header
provided in

     http://www.itk.org/HTML/Data.htm


Details about the entire list of file formats supported
by ITK are available in the FAQ entry


http://www.itk.org/cgi-bin/InsightFAQ/InsightFAQ?req=show&file=faq01.007.htp


Before running this application with your own data
you may want to practice with the BrainWeb data that
is available at our ftp server

   ftp://public.kitware.com/pub/itk/Data/BrainWeb

Note that they are just the files downloaded from
the BrainWeb server plus the corresponding MetaImage
headers.

In particular you may want to try the two images
contained in the following tar.gz files:


   BrainPart1.tgz
   BrainPart1Rotated10Translated15.tgz




  Regards,



    Luis



-----------------------------
Christos Panagiotou wrote:

> guys
> 
> i have a problem testing the MultiResMIRegistration
> 
> I have some raw volumes stored in single files ( i downloaded also a 
> sample from http://www.bic.mni.mcgill.ca/brainweb/selection_normal.html 
> as suggested)
> 
> I run the application and i get the following error messages:
> 
> -------------------------------ERROR----------------------------------
> 
> ./MultiResMIRegistration ~/PhD/Data/raw/test.txt
> Parsing input ...
> Fixed image filename: 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> Big Endian: 0
> Image Size: [181, 217, 181]
> Image Spacing: [1, 1, 1]Moving image filename: 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> Big Endian: 0
> Image Size: [181, 217, 181]
> Image Spacing: [1, 1, 1]Permute order: [0, 1, 2]Flip axes: [0, 0, 
> 0]Number of levels: 5
> Fixed image shrink factors: [4, 4, 1]Moving image shrink factors: [8, 8, 
> 1]Number of iterations: [2500, 2500, 2500, 2500, 2500]Learning rates: 
> [1e-04, 1e-05, 5e-06, 1e-06, 5e-07]Translation scale: 320
> PGM directory: /home/christos/PhD/Data/raw/pgm
> 
> Error while reading in fixed image.
> Error occured during registration
> itk::ExceptionObject caught
> 
> itk::ImageFileReaderException (0x9470288)
> Location: "Unknown"
> File: /home/christos/Applications/ITK/Code/IO/itkImageFileReader.txx
> Line: 101
> Description:  Could not create IO object for file 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 
> 
> Caught an ITK exception:
> 
> itk::ImageFileReaderException (0x9470288)
> Location: "Unknown"
> File: /home/christos/Applications/ITK/Code/IO/itkImageFileReader.txx
> Line: 101
> Description:  Could not create IO object for file 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 
> -------------------------------ERROR----------------------------------
> 
> the input file is just an alteration of the sample inputs where i 
> altered the paths and some other info s.a. volume xyz sizes, the pgm 
> output dir etc.
> 
> i also paste the input file incase i did something wrong there and i 
> cant see it...
> 
> --------------------------------input--------------------------------------
> 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 0
> 181 217 181
> 1.0 1.0 1.0
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 0
> 181 217 181
> 1.0 1.0 1.0
> 0 1 2
> 0 0 0
> 5
> 4 4 1
> 8 8 1
> 2500 2500 2500 2500 2500
> 1e-4 1e-5 5e-6 1e-6 5e-7
> 320
> /home/christos/PhD/Data/raw/pgm
> 
> --------------------------------input--------------------------------------
> 
> as you see i am using the same volume however i tried also with 
> different volumes from the brainweb and alternate sources...
> 
> any suggestions would be appreciated
> 
> thanks
> christos
>