Plastimatch threshold-based segmentation

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Yalçın Kuzay

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Nov 10, 2022, 9:27:07 AM11/10/22
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Dear All,

I recently use Plastimatch 1.9.4.

when I try to create segmentation (via threshold), the upper-threshold option does not work. Any idea?

I use following command:  plastimatch segment --input Fixed.nii.gz --lower-threshold -1000 --upper-threshold -512 --output-img Fixed_body_mask.nii



Thanks in advance
Yalcin

Sharp, Gregory C.

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Nov 10, 2022, 11:13:30 AM11/10/22
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Hi Yalcin,

That option does not appear to be implemented. The plastimatch segment command is a bit quirky. Maybe you can explain your goal and I can advise an alternative.

Greg

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Subject: [Plastimatch] Plastimatch threshold-based segmentation

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Yalçın Kuzay

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Nov 10, 2022, 12:25:25 PM11/10/22
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Hi Greg,

Thanks for your reply. 

I recently register some lung CTs. To able to create dice similarity coefficient, I need masks. I plan to create automated segments (as a mask) for bone, water and soft tissue by using threshold. Then, I will compare the dice between fixed image's masks and transformed image's mask.

I'm unsure if Dice can work without making ay regions.

Best regards

Yalçın 

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Sharp, Gregory C.

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Nov 10, 2022, 1:10:13 PM11/10/22
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Hi Yalcin,

Yes, you do need two binary (0 or 1) images for the dice.

The segment command does special processing to find the body contour, including filling holes and the like. It's kind of peculiar and difficult to use. What you want instead is the threshold command.

plastimatch threshold --range "-1000,-512" --input Fixed.nii.gz --output Fixed_body_mask.nii

That is the syntax, but the range of values will include a bunch of air outside of the body. You'll probably want to test out different ranges until you get something useful.

Greg

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From: plast...@googlegroups.com <plast...@googlegroups.com> on behalf of Yalçın Kuzay <ylc...@gmail.com>
Sent: Thursday, November 10, 2022 12:25 PM
To: plast...@googlegroups.com
Subject: Re: [Plastimatch] Plastimatch threshold-based segmentation

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Hi Greg,

Thanks for your reply.

I recently register some lung CTs. To able to create dice similarity coefficient, I need masks. I plan to create automated segments (as a mask) for bone, water and soft tissue by using threshold. Then, I will compare the dice between fixed image's masks and transformed image's mask.

I'm unsure if Dice can work without making ay regions.

Best regards

Yalçın

On Thu, 10 Nov 2022, 17:13 Sharp, Gregory C. <GCS...@partners.org<mailto:GCS...@partners.org>> wrote:
Hi Yalcin,

That option does not appear to be implemented. The plastimatch segment command is a bit quirky. Maybe you can explain your goal and I can advise an alternative.

Greg

________________________________________
From: plast...@googlegroups.com<mailto:plast...@googlegroups.com> <plast...@googlegroups.com<mailto:plast...@googlegroups.com>> on behalf of Yalçın Kuzay <ylc...@gmail.com<mailto:ylc...@gmail.com>>
Sent: Thursday, November 10, 2022 9:27 AM
To: Plastimatch
Subject: [Plastimatch] Plastimatch threshold-based segmentation

External Email - Use Caution

Dear All,

I recently use Plastimatch 1.9.4.

when I try to create segmentation (via threshold), the upper-threshold option does not work. Any idea?

I use following command: plastimatch segment --input Fixed.nii.gz --lower-threshold -1000 --upper-threshold -512 --output-img Fixed_body_mask.nii



Thanks in advance
Yalcin

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Yalçın Kuzay

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Nov 10, 2022, 1:38:25 PM11/10/22
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Hi Greg, 

What do you meen with bunch of air outside of the body. How it can influence the quality of your the Dice?

 Best


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Sharp, Gregory C.

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Nov 10, 2022, 2:13:39 PM11/10/22
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Hi Yalcin,

I'm assuming this is CT.  In your original command, it looks like you were trying to include the range -512 to -1000.  This range will include a fair portion of air, assuming air is present in the scan.

Greg

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Yalçın Kuzay

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Nov 10, 2022, 4:17:51 PM11/10/22
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Hi Greg,

Since I wanted to see the agreement of the lung, I have determined those parameters. Is it better to go with -512 to 1000 for the body or 300 to 1000 for bone density? Which mask (density) could work for the chest CT?

Best
Yalcin

Sharp, Gregory C. <GCS...@partners.org>, 10 Kas 2022 Per, 20:13 tarihinde şunu yazdı:


--
Yalçın KUZAY, PhD

Sharp, Gregory C.

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Nov 14, 2022, 4:52:45 PM11/14/22
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Hi Yalcin,
Sounds good. As long as you are getting good segmentations, all is well.
Greg

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From: plast...@googlegroups.com <plast...@googlegroups.com> on behalf of Yalçın Kuzay <ylc...@gmail.com>
Sent: Thursday, November 10, 2022 4:17 PM
To: plast...@googlegroups.com
Subject: Re: [Plastimatch] Plastimatch threshold-based segmentation

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Hi Greg,

Since I wanted to see the agreement of the lung, I have determined those parameters. Is it better to go with -512 to 1000 for the body or 300 to 1000 for bone density? Which mask (density) could work for the chest CT?

Best
Yalcin

Sharp, Gregory C. <GCS...@partners.org<mailto:GCS...@partners.org>>, 10 Kas 2022 Per, 20:13 tarihinde şunu yazdı:
Hi Yalcin,
I'm assuming this is CT. In your original command, it looks like you were trying to include the range -512 to -1000. This range will include a fair portion of air, assuming air is present in the scan.
Greg


From: plast...@googlegroups.com<mailto:plast...@googlegroups.com> <plast...@googlegroups.com<mailto:plast...@googlegroups.com>> On Behalf Of Yalçin Kuzay
Sent: Thursday, November 10, 2022 1:38 PM
To: plast...@googlegroups.com<mailto:plast...@googlegroups.com>
Subject: Re: [Plastimatch] Plastimatch threshold-based segmentation


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Hi Greg,

What do you meen with bunch of air outside of the body. How it can influence the quality of your the Dice?

Best

On Thu, 10 Nov 2022, 19:10 Sharp, Gregory C. <GCS...@partners.org<mailto:GCS...@partners.org>> wrote:
Hi Yalcin,

Yes, you do need two binary (0 or 1) images for the dice.

The segment command does special processing to find the body contour, including filling holes and the like. It's kind of peculiar and difficult to use. What you want instead is the threshold command.

plastimatch threshold --range "-1000,-512" --input Fixed.nii.gz --output Fixed_body_mask.nii

That is the syntax, but the range of values will include a bunch of air outside of the body. You'll probably want to test out different ranges until you get something useful.

Greg

________________________________________
Sent: Thursday, November 10, 2022 12:25 PM
To: plast...@googlegroups.com<mailto:plast...@googlegroups.com>
Subject: Re: [Plastimatch] Plastimatch threshold-based segmentation

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Hi Greg,

Thanks for your reply.

I recently register some lung CTs. To able to create dice similarity coefficient, I need masks. I plan to create automated segments (as a mask) for bone, water and soft tissue by using threshold. Then, I will compare the dice between fixed image's masks and transformed image's mask.

I'm unsure if Dice can work without making ay regions.

Best regards

Yalçın

On Thu, 10 Nov 2022, 17:13 Sharp, Gregory C. <GCS...@partners.org<mailto:GCS...@partners.org><mailto:GCS...@partners.org<mailto:GCS...@partners.org>>> wrote:
Hi Yalcin,

That option does not appear to be implemented. The plastimatch segment command is a bit quirky. Maybe you can explain your goal and I can advise an alternative.

Greg

________________________________________
From: plast...@googlegroups.com<mailto:plast...@googlegroups.com><mailto:plast...@googlegroups.com<mailto:plast...@googlegroups.com>> <plast...@googlegroups.com<mailto:plast...@googlegroups.com><mailto:plast...@googlegroups.com<mailto:plast...@googlegroups.com>>> on behalf of Yalçın Kuzay <ylc...@gmail.com<mailto:ylc...@gmail.com><mailto:ylc...@gmail.com<mailto:ylc...@gmail.com>>>
Sent: Thursday, November 10, 2022 9:27 AM
To: Plastimatch
Subject: [Plastimatch] Plastimatch threshold-based segmentation

External Email - Use Caution

Dear All,

I recently use Plastimatch 1.9.4.

when I try to create segmentation (via threshold), the upper-threshold option does not work. Any idea?

I use following command: plastimatch segment --input Fixed.nii.gz --lower-threshold -1000 --upper-threshold -512 --output-img Fixed_body_mask.nii



Thanks in advance
Yalcin

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