[Gate-users] Voxelised Source Placement Confusion

Fri Jul 15 22:26:23 CEST 2022

Hi everyone,

I was not able to reproduce the incorrect behavior in later tests with the same macros and voxelized source, so interfile also seems to work just fine in 9.2. I did update ROOT to a newer version before the new tests, but I doubt it should have any effect in this case. I guess there might be a certain combination that causes issues, but at the moment I have no idea what might have been the cause.

In a nutshell, using interfile is completely viable too.

As a sidenote, I don't think the size of the CT/phantom voxels/matrix should have any effect on the source position, but it can cause wrong attenuation if the anatomic locations are in different locations.

Regards,
Ville-Veikko Wettenhovi
________________________________
From: Julia Franziska Brosch-Lenz <jbrosch at bccrc.ca>
Sent: Friday, July 15, 2022 21:37
To: 'BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)' <mark.baker23 at nhs.net>; Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi>; gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: RE: Voxelised Source Placement Confusion

Hi Mark, hi Ville-Veikko,

I can confirm that there is no issue with the voxelized source shift in Gate version 9.2 when you use mhd files.

I highly recommend to convert your files to mhd format that should ease it for you. Plus I noticed your PET and CT are not having the same voxel and matrix size. This is an issue too, they not only have to be registered, but also resampled to the same voxel and matrix size. Then you need to shift the source image (=PET in your case) by half of it’s size.

I attach the example that I gave you in my answer to your previous email back in April again:

Here an example from one of my simulations: my source image matrix is 256x256x1000. My voxel size is 0.145x0.145x0.145 mm^3. That makes a total image size of 37.12 37.12 145 mm^3. That means the command line for my source is:

# Source has always to be shifted to -1/2 of its total length in x,y,z

/gate/source/YOURSOURCE/setPosition -18.56 -18.56 -72.5 mm

Please try 1) resample your CT to PET size and then 2) convert PET and resampled CT to mhd format, and 3) apply the shift as explained above. You should not encounter any issue anymore.

Best,

Julia

From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> On Behalf Of BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)
Sent: July 15, 2022 8:45 AM
To: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi>; gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Voxelised Source Placement Confusion

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Hi Ville-Veikko

Apologies for the delay in replying. Between leave and short-staffing in my department, I’ve not been able to get back to my project for a while. I think I’m using version 9.0 but I would have to check.

I have a plan to try both approaches (interfile and rolling back to 8.2) and I’ll report back with my own findings. Probably won’t be until the end of next week unfortunately though.

Thank you

Mark Baker

Principal Clinical Scientist

Imaging Physics (Ionising)

The Clatterbridge Cancer Centre NHS Foundation Trust

(he, him)

CCCW Tel:  0151 556 5030

CCCL Tel: 0151 318 8438

Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>

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From: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>
Sent: 12 July 2022 16:32
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: Voxelised Source Placement Confusion

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Hi Mark,

Have you had any progress? What GATE version are you using by the way? I did some tests myself, and it seems that voxelized sources are either broken in GATE v9.2 or then the documentation is outdated. The shift that worked previously (at least in 8.2), now shifts the source in completely different location. In fact, using the original rule, the source seems to be shifted completely out of the scanner FOV in the current version.

Has the voxelized source example been tested/validated for the current version?

Regards,

Ville-Veikko Wettenhovi

________________________________

From: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>
Sent: Wednesday, June 29, 2022 10:59
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: Re: Voxelised Source Placement Confusion

Hi Mark,

Sorry for the late response. I've not used DICOM images myself with GATE ever so I really can't comment them. One possibility is if you convert the DICOM images into interfile or MetaImage files and then try again. Those have always worked fine in my case.

Regards,

Ville-Veikko Wettenhovi

________________________________

From: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>
Sent: Thursday, June 23, 2022 14:55
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>; Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: RE: Voxelised Source Placement Confusion

Hi Ville-Veikko (and everyone else)

Apologies for the delay in getting this data back, I’ve not had much project time recently. I’ve attached a single slice from each of the PET and CT data, and as far as I can tell, the data looks correct.

Thank you

Mark Baker

Principal Clinical Scientist

Imaging Physics (Ionising)

The Clatterbridge Cancer Centre NHS Foundation Trust

(he, him)

CCCW Tel:  0151 556 5030

CCCL Tel: 0151 318 8438

Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>

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From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> On Behalf Of BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)
Sent: 17 June 2022 09:27
To: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Voxelised Source Placement Confusion

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I think so. I got the information direct from the header files, with both imageJ and Weasis. I’m away from my data at the moment, but when I am back I’ll attach a sample slice with the header attached, in case I’m being a complete numpty.

Thank you

Mark Baker

Principal Clinical Scientist (Interim)

Imaging Physics (Ionising)

The Clatterbridge Cancer Centre NHS Foundation Trust

(he, him)

CCCW Tel:  0151 556 5030

CCCL Tel: 0151 318 8438

Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>

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From: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>
Sent: 16 June 2022 15:23
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: Voxelised Source Placement Confusion

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Hi Mark,

The macros seem fine. Are you sure the relevant dimensions and the size of voxels are present and correct in the PET data header file?

Regards,

Ville-Veikko Wettenhovi

________________________________

From: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>
Sent: Thursday, June 16, 2022 17:08
To: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: RE: Voxelised Source Placement Confusion

Hi Ville-Veikko

Thank you for your reply. The relevants macs are attached to this email. I have 8 mains in total (one for each core) which are identical apart from the first one has visualisation. The current offset was just something I was trying but I can’t seem to get any of the numbers to truly work.

Thank you

Mark Baker

Principal Clinical Scientist

Imaging Physics (Ionising)

The Clatterbridge Cancer Centre NHS Foundation Trust

(he, him)

CCCW Tel:  0151 556 5030

CCCL Tel: 0151 318 8438

Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>

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From: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>
Sent: 16 June 2022 14:46
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: Voxelised Source Placement Confusion

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Hi Mark,

Moving the voxelized source by half of each dimension should indeed work and has worked in the cases where I've used voxelized source. Could you share the part of the macro where you define and move the voxelized source?

Another way to determine the positioning could be to form the "ground truth" image of the trues, i.e. an image where the coincidences are accumulated based on their source locations. Then compare that image to the attenuation image from the attenuation map actor (both with the same dimensions).

Regards,

Ville-Veikko Wettenhovi

________________________________

From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> on behalf of BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>
Sent: Thursday, June 16, 2022 16:27
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: [Gate-users] Voxelised Source Placement Confusion

Hi all

I raised this query a while (or one similar) but unfortunately, I’ve not managed to get back around to my project for a while. In short, I can’t get good alignment between my CT and PET images. My understanding is that the voxelised PET source image should be offset by half of its size to account for it being placed in the corner of the world instead of the centre where the CT image is place. My world is 1 1 2 m and my CT data is 780 780 693 mm (512x512x213 matrix). My PET data is 814.568 814.568 639 mm (200x200x213 matrix).

I think I was a bit confused at first, and was moving the PET source by half of its own size but then I re-read the ReadTheDocs and I think it is suggesting that I actually need to move the PET image by half of the world size (setPosition -500 -500 -1000 mm) but this results in a large offset. I’ve tried various combinations of half the size of the world, half the size of the PET data etc. and I think I’m just going around in circles now. Logically, I feel like the solution is that I move half of the world size at first to move the corner of the PET data into the centre of the world, then back by half of the PET image to put the centre of the PET in the centre of the world, but it is still offset. Any suggestions, as I’m tearing my hair out a little now.

Additionally, in order to test where the positioning is correct, I’m relying on the generation of secondary electrons within the water phantom in my image and looking at the NbofHits file produced. This works fine when the difference is obvious between the two, but I wonder if there is a better way to see the isocentre in order to 100% confirm it is correct? The reason I use secondary electrons is that positrons and gammas flood the image making it impossible to see the underlying CT data, plus I expect the secondary electrons to largely be created in the water and not air.

Thank you in advance!

Mark Baker

Principal Clinical Scientist

Imaging Physics (Ionising)

The Clatterbridge Cancer Centre NHS Foundation Trust

(he, him)

CCCW Tel:  0151 556 5030

CCCL Tel: 0151 318 8438

Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>

Microsoft Teams (click here)<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7C3c8b9c8490ec4c9053c408da66911aa4%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637935070802141353%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UkmV%2B4%2FhEF5RJVprLCwhMGSSrr1%2FxS6Yu6Sn9pNBkXc%3D&reserved=0>

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University of Liverpool

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