CT scan and coordinates. Help!
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Hello everyone,
I've been learning Fiji to analyze the data for my thesis and I need some help. I am working with three plane CT scans (coronal, sagittal, transverse) and measuring different skeletal elements. I have been using the reslice tool to get all three planes to scroll independently. Unfortunately the X, Y, Z coordinates are not global, they change with each plane view (i.e. x = 0 on the left side of the slice no matter which view I am in). I need them to correspond in all three planes in order to do the calculations needed. How can I do this? After days of messing around, I still can't seem to make it happen. Thank you in advance for any desperately needed guidance. -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: CT scan and coordinates. Help!
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Hello there,
Greetings, Before you resliced, did you try to set the scale as global (check this option). Hopefully this might work Heartiest Desideratum, Yours Truly, Hamzah M. Beakawi Al-Hashemi, S.M.ASCE RSO | B.Sc. | M.Sc. Candidate | Civil (Geotechnical) Engineering King Fahd University of Petroleum & Minerals (KFUPM) College of Engineering Sciences and Applied Engineering Civil and Environmental Engineering Department Geotechnical Engineering Division KFUPM Main Campus | Bldg. 16 | Dhahran 31261| Saudi Arabia Mob: +966 (0) 542724747 Emails: [hidden email] | [hidden email] ORCID: 0000-0002-3991-1712 LinkedIn: Https://www.Linkedin.Com/In/Hamzah-M-Al-Hashemi-0961a984 ResearchGate: Https://www.Researchgate.Net/Profile/Hamzah_Al-Hashemi -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of KaraokeMary Sent: Tuesday, February 6, 2018 7:41 AM To: [hidden email] Subject: CT scan and coordinates. Help! Hello everyone, I've been learning Fiji to analyze the data for my thesis and I need some help. I am working with three plane CT scans (coronal, sagittal, transverse) and measuring different skeletal elements. I have been using the reslice tool to get all three planes to scroll independently. Unfortunately the X, Y, Z coordinates are not global, they change with each plane view (i.e. x = 0 on the left side of the slice no matter which view I am in). I need them to correspond in all three planes in order to do the calculations needed. How can I do this? After days of messing around, I still can't seem to make it happen. Thank you in advance for any desperately needed guidance. -- Sent from: https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimsva91-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttp%253a%252f%252fimagej.1557.x6.nabble.com%26umid%3DD739B480-6483-ED05-B5E9-97DD893D7CB9%26auth%3Dec34f7633709e8bd85e48c7fc0c92c09c079e558-069d74f2c1a015c180ac663cf35014a7fb55b89d&data=01%7C01%7Cg201552950%40kfupm.edu.sa%7Cf80bec4ac8064f19bf1508d56d1d3f25%7Cfe555c43628d49c6b104c175570a6776%7C1&sdata=XlcwfEIvnSHd8cSnlEIdWzDOaSnyJQrOC55xLxIgvqE%3D&reserved=0 -- ImageJ mailing list: https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimsva91-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttp%253a%252f%252fimagej.nih.gov%252fij%252flist.html%26umid%3DD739B480-6483-ED05-B5E9-97DD893D7CB9%26auth%3Dec34f7633709e8bd85e48c7fc0c92c09c079e558-e041496a5044ce28e0e80b67970c54bda6b1ffe7&data=01%7C01%7Cg201552950%40kfupm.edu.sa%7Cf80bec4ac8064f19bf1508d56d1d3f25%7Cfe555c43628d49c6b104c175570a6776%7C1&sdata=pavWQjg%2FgeZq8StxtG4z2GXyqBvDUxWGAtC1RWk8asQ%3D&reserved=0 ======================================================= This message has been analyzed by KFUPM Deep Discovery Email Inspector. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: CT scan and coordinates. Help!
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I did, and it sets my 1.7mm/pixel scale, but unfortunately does nothing to
the coordinate system. -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: CT scan and coordinates. Help!
Re: CT scan and coordinates. Help!
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In reply to this post by KaraokeMary
If I understand correctly, you'd like to have a three-pane view with
orthogonal planes, where each plane is referring to the original stack coordinates? I.e. xy, xz and yz? To my knowledge, this is not possible with the ImagePlus and ImageStack classes. The *Image > Stacks > Orthogonal Views* plugin is as far as it gets in plain ImageJ. You might however want to have a look at BigDataViewer [1] and what others achieve with it, e.g. BigWarp [2] and BigCat [3]. You'll have to dive into some scripting however... Cheers Jan [1]: https://imagej.net/BigDataViewer [2]: https://imagej.net/BigWarp [3]: https://github.com/saalfeldlab/bigcat On 06.02.2018 05:40, KaraokeMary wrote: > Hello everyone, > > I've been learning Fiji to analyze the data for my thesis and I need some > help. I am working with three plane CT scans (coronal, sagittal, transverse) > and measuring different skeletal elements. I have been using the reslice > tool to get all three planes to scroll independently. Unfortunately the X, > Y, Z coordinates are not global, they change with each plane view (i.e. x = > 0 on the left side of the slice no matter which view I am in). I need them > to correspond in all three planes in order to do the calculations needed. > How can I do this? After days of messing around, I still can't seem to make > it happen. > > Thank you in advance for any desperately needed guidance. > > > > -- > Sent from: http://imagej.1557.x6.nabble.com/ > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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