[Gate-users] Hoffmann brain phantom- GATE can't read interfile

[Chen, Yu]

Hi, Daniel,

I guess you should copy the data file "hof3.i33"
to your current dir "./".

For
"Error: Could not open header file 'hof3.i33'!"

I guess it is just a typo in gate code, may should be data file not header file.

Actually, a good practice in GATE is to copy all necessary files 
(e.g., GateMaterials.db, all macros, all header and data files) 
in running dir, and to check and modify respect dependency before running
a job.

Hope it is the case. Good lucky. 

Yu Chen, Ph.D.
University of Massachusetts Medical School
Division of Nuclear Medicine
55 Lake Avenue North
Worcester, MA 01655-0243
Phone:  (508) 856-6123
Fax:    (508) 856-4572



-----Original Message-----
From: gate-users-bounces at lists.healthgrid.org on behalf of Daniel Woodsworth
Sent: Tue 6/5/2007 5:47 PM
To: gate-users at lists.healthgrid.org
Subject: [Gate-users] Hoffmann brain phantom- GATE can't read interfile
 
Hi,

I am trying to run a simulation of a digital Hoffmann brain phantom. I am
using the Interfile data distributed with GATE (found in
$GATEHOME/examples/example_PHANTOM_SOURCE/Voxelized_Phantom_Source). When
I try to read the interfile into GATE I get:

PreInit> /gate/hof_brain/interfileReader/readFile ../hoffmann_data/hof3.h33
/gate/hof_brain/interfileReader/readFile ../hoffmann_data/hof3.h33
 Header read from       '../hoffmann_data/hof3.h33'
 Data file name         'hof3.i33'
 Nb of planes:           55
 Nb of pixels per plane: 128 128
 Pixel size:             2.000e+00 2.000e+00
 Slice thickness:        2.000e+00
 Matrix size:            2.560e+02 2.560e+02
 Data type:              UNSIGNED INTEGER


Error: Could not open header file 'hof3.i33'!
PreInit>

I have looked at the hof3.i33 file (using matlab to read in the binary)
and it seems completely uncorrupted. Does anyone know how to fix this
problem? I wonder why it says could not open header file 'hof3.i33' when
the .i33 file is in fact not the header (which is the .h33 file) and
rather is the binary file? The .h33 file and the .i33 file are in the same
directory and GATE seems to read the header file fine, so I don't think it
is simply an access problem. I pasted my macro below (it is essentially
the same as the GATE example).

Thanks for any help.

Daniel


###############################################################################
#Phantom Macro. (phan.mac)
###############################################################################

#Create and intialize a voxellized object.
/gate/world/daughters/name hof_brain
/gate/world/daughters/insert parameterizedBoxMatrix

#Tell GATE to get ready to read an interfile.
/gate/hof_brain/geometry/insertReader interfile
/gate/hof_brain/interfileReader/insertTranslator range

#GATE now reads in a table which contains a greyscale range, with a
#corresponding attenuation coefficient. It tells GATE what attenuation values
#to assign to the greyscale pixels.
/gate/hof_brain/interfileReader/rangeTranslator/readTable
../hoffmann_data/range.dat
/gate/hof_brain/interfileReader/rangeTranslator/describe 1

#Now read the interfile and perform the mapping.
/gate/hof_brain/interfileReader/readFile  ../hoffmann_data/hof3.h33

#Attach VoxelPhantomSD- toolkit so GATE can track particle interactions in
the
#Phantom. Note that it must be Voxel, not normal PhantomSD
/gate/hof_brain/attachVoxelPhantomSD


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