Hi Yalcin,
Sounds good. As long as you are getting good segmentations, all is well.
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
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
From:
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plast...@googlegroups.com<mailto:
plast...@googlegroups.com>> <
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plast...@googlegroups.com><mailto:
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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
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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
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