The Visible Human Dataset

[Tim C]

Hi,

I’m looking to visualise the CT and MRI data from the Visible Human
data set using ITK-snap so I can then segment the Pelvic and upper leg
regions for simulation purposes. I’m having trouble loading the
visible human data into ITK-Snap as it is in a 2D raw format which
doesn’t seem to be compatible with ITK-Snap.

If I understand correctly ITK is an open-source software system to
support the Visible Human Project and ITK-Snap is program derived from
this. I assumed therefore that I should be able to load the data
straight into ITK-Snap. Am I doing something stupid or do I need to
convert the raw Visible Human slices to a different format to load
them into ITK-Snap? Has anyone done this successfully and have any
recommendations how should I go about the conversion?

Thank you in advance for any advice you can give me.

Thanks for your time, Tim C

[stue...@mpi-cbg.de]

Hello Tim,

it should be possible to load raw data into ItkSnap,
just choose Raw File in the open dialog. You will have to
enter the header size (offset where binary data begins)
and the x,y,z-dimensions of the data set.
What kind of problems do you have loading the data?
The Raw File Reader had a bug resulting in a segmentation
fault in a previous version, I'm not sure if the bug still
exists in the new version.
However, if you can compile ItkSnap on your own you
can fix the bug by yourself. I posted a quick bug fix
some time ago on this list.

Regards,
Jan Stühmer

[Tim C]

Hi Jan,

Thanks for your quick response!
I'm having problems as the files provided in the Visible human data
set which I’m trying to use are a set of 2D raw images. As far as I
know these can’t be directly loaded into ITK-Snap?

Regards
Tim Coles

[Félix Manuel Córdoba tuta]

Hi,
the CT and MRI data from the Visible Human Project aren't in raw format, these are DICOM.

2008/5/15 Tim C <timoth...@iit.it>:

--
Félix Manuel Córdoba Tuta
Investigación y Desarrollo
Numérica Ltda
fcor...@numerica.com.co
Calle 46 #33-18 Of 302
Teléfono: ++57 (7) 6576894 ext 107
TeleFax: ++57 (7) 6436501
Celular: 3002072625 - 3108082442
Bucaramanga - Santander - Colombia

[Tim C]

Ah, I read somewhere the data was a Raw data set! I thought a DICOM
file was a single file? I have two files, a header and an image. Could
you explain how I can load the Visible Human data into ITK-Snap? I'll
try to explain what I have, could you tell me if this is what you
expected?

I have downloaded two files for the frozenCT Visible human data set,
one file "frozenCT" contained files named c_vm1006.fro.Z with varying
numbers which I have uncompressed to c_vm1006.fro.
The other file "frozenCTHeaders" contains header files named
c_vm1006.fro.txt with varying numbers corresponding to the images. The
length of each header is 3416. Should DICOM data not be represented in
a single file? do I need to pre process this data? Can you recommend a
program to do so?

Thanks again, Tim

[Félix Manuel Córdoba tuta]

Tim,

In ITK-Snap 1.6 you can load individual files *.fro, from radiological VHP DataSet.

Menu: Flile -> Open -> Grayscale Image (Ctrl-G)
then fill the fields:
Image file name: Select the file *.fro (ex: c_vm1150.fro)
Image file format: Select GE Version 5 file

I don't kown how to load a file serie, although some files load a serie of 3.

2008/5/16 Tim C <timoth...@iit.it>:

[Mik Gangal]

Don't know if anybody still reading this thread..

Just wondering if there's any way to load the MRI files to itk-snap or 3dslicer..

especially the .t1 .t2 .pd file formats..nothing can open them

Thank you so much