RE: [fluka-discuss]: DICOM Import Explanation

From: Vasilis Vlachoudis <Vasilis.Vlachoudis_at_cern.ch>
Date: Thu, 26 Mar 2015 15:45:23 +0000

Right, you cannot reduce the number of VOXEL### regions as flair is right now.
One possible implementation for the future would be that if the user
doesn't provide a correction for the density to assign one region
per HU interval.

V.

________________________________
From: Bartkoski,Dirk Alan [DABartkoski_at_mdanderson.org]
Sent: 26 March 2015 14:41
To: Vasilis Vlachoudis; Mary Chin; fluka-discuss_at_fluka.org
Subject: RE: [fluka-discuss]: DICOM Import Explanation

I think I understand. So there is no way to reduce the number of VOXEL### regions, only to reduce the number of materials.

________________________________
Dirk A. Bartkoski, Ph.D.
Postdoctoral Fellow | Radiation Physics
[MDACC Logo]
Mays Clinic (ACBP1.2972.1)
1515 Holcombe Blvd., Unit 1202
Houston, TX 77030
(713) 745-8124 Office | (865) 310-7349 Mobile
dabartkoski_at_mdanderson.org<mailto:dabartkoski_at_mdanderson.org>

From: Vasilis Vlachoudis [mailto:Vasilis.Vlachoudis_at_cern.ch]
Sent: Thursday, March 26, 2015 2:51 AM
To: Bartkoski,Dirk Alan; Mary Chin; fluka-discuss_at_fluka.org
Subject: RE: [fluka-discuss]: DICOM Import Explanation

Hi

this is correct, flair will assigning a new region for each hounsfield unit, while groups of them will share the same materials.
The reason is that the additional CORRFACTor has to be applied per hounsfield unit to take in to account the
continuous variation of the density.

The material and corrfactor will be embded in the voxel file.

Vasilis
________________________________
From: owner-fluka-discuss_at_mi.infn.it<mailto:owner-fluka-discuss_at_mi.infn.it> [owner-fluka-discuss_at_mi.infn.it] on behalf of Bartkoski,Dirk Alan [DABartkoski_at_mdanderson.org]
Sent: 25 March 2015 18:05
To: Mary Chin; fluka-discuss_at_fluka.org<mailto:fluka-discuss_at_fluka.org>
Subject: RE: [fluka-discuss]: DICOM Import Explanation
It does generate a .vxl. Isn't it supposed to generate the same number of voxel-regions as I have specified in my .mat file? For example if my .mat file has four HU ranges corresponding to four materials then flair should generate six regions VOXEL, VOXEL001, VOXEL002, VOXEL003, VOXEL004, VOXEL005, and VOXEL006. Where the last four correspond to my four material regions. This is not happening. It is generating a separate region for almost every single HU value in the DICOM image.

Furthermore, I am unclear about the material definitions. Are the material definitions that I specify in the DICOM tab with .inp embedded in the .vxl file or do I also need to define all of materials in the main input file I am using as my FLUKA run input?
________________________________
Dirk A. Bartkoski, Ph.D.
Postdoctoral Fellow | Radiation Physics
[MDACC Logo]
Mays Clinic (ACBP1.2972.1)
1515 Holcombe Blvd., Unit 1202
Houston, TX 77030
(713) 745-8124 Office | (865) 310-7349 Mobile
dabartkoski_at_mdanderson.org<mailto:dabartkoski_at_mdanderson.org>

From: me_at_marychin.org<mailto:me_at_marychin.org> [mailto:me_at_marychin.org]
Sent: Tuesday, March 24, 2015 5:05 PM
To: Bartkoski,Dirk Alan; fluka-discuss_at_fluka.org<mailto:fluka-discuss_at_fluka.org>
Subject: Re: [fluka-discuss]: DICOM Import Explanation

Hi Dirk,

For voxel geometry we have the following files:

.inp -- as in all other FLUKA simulations, with or without voxels.

.mat -- a lookup table so that FLAIR may map your DICOM files to a .vxl file. This table is what the medical physics community refers to as the 'conversion ramp'.

.vxl -- generated automatically by FLAIR for us, although in principle one can still generate this manually without FLAIR's help, the painful way, in which case .mat would not be necessary.

The material.inp which comes with the standard FLAIR distribution contains the MATERIAL and COMPOUND cards only. Therefore, it is only an excerpt. It is not yet the complete .inp ready for a FLUKA run. We can see that each SDUM in the MATERIAL card corresponds to an entry in the second column of .mat.

Did you get a newly created file with, .vxl extension, in your directory? Organ and voxel-regions numbers are embedded in .vxl. If we let FLAIR does the conversion for us, these are nothing we need to worry about. We just need to specify the name of the .vxl file as SDUM for the VOXELS card in .inp.

:) mary

On 24 March 2015 at 09:57 "Bartkoski,Dirk Alan" <DABartkoski_at_mdanderson.org<mailto:DABartkoski_at_mdanderson.org>> wrote:
I have been trying to import CT DICOM images using flair. I can import them and look at the slices. I have opened the head.mat and material.inp example files. There are a few things I do not understand about the process as explained in the online "Voxel and Medical Applications" slides.

1. I do not understand the meaning of "voxel-region number". In the .mat file you specify the HU value ranges that belong to each material that is specified in the material.inp file. I do not where or how the voxel-region number is supposed to be assigned.

2. flair is supposed to generate regions based on the organ number. This does not happen. I assume it because I can't figure out how to assign organ numbers.

Any clarity or direction to additional tutorial resources or examples would be most appreciated.

________________________________
Dirk A. Bartkoski, Ph.D.
Postdoctoral Fellow | Radiation Physics
[MDACC Logo]
Mays Clinic (ACBP1.2972.1)
1515 Holcombe Blvd., Unit 1202
Houston, TX 77030
(713) 745-8124 Office | (865) 310-7349 Mobile
dabartkoski_at_mdanderson.org<mailto:dabartkoski_at_mdanderson.org>







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Received on Thu Mar 26 2015 - 18:03:29 CET

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