as you made the transition from tutorial 1, you skipped over the actual file selection, which may be 'trivial', but, where do you get the data? can you import/link from an existing database, like osirix or Horus? now, in tutorial 2, you suddenly have data in the Dicom browser.
Thank you so much for all your videos. I wanted to ask. is there somewhere an explanation regarding on how to cut and use the slicer with an STL file extracted from solid?
Using the ruler function. How would I go about keeping it on the screen whilst scrolling through the model so I can line up other measurements with that one?
Great Video... how do u identify which segment is which part of heart or any other organ. I mean for someone who does not know where is arota or what is its location, how should they handle the situation?
Hi, honestly, it's best to find a radiologist or another expert who could teach you how to read the images and identify anatomical structures. Alternatively, you can look online for anatomical atlases.
ok, now, it would be useful to point out that you are scrolling through the series with that bar at the top of each view ... in segmentation editor, you said, click 'undo', where is it? when first painting the aorta, it was not visible, or explained, how you moved through the slices, as you painted... so, unlike the painting tool, threshold works in all slices, simultaneously. the 'painting-type' tools work in only one slice at a time?
Does anyone know a nifty way to fill the inside of ring (maybe a couple of rings in the stack are incomplete)? Or is there a useful tutorial for that? I have a fiber data that I would like to render. The signal intensity of its edge is bright, making it easier to segment. However, the signal intensity of inside and outside (i.e. air) of fiber is almost the same. That returns the segmentation result of a tube rather than a cylinder.
I am working with images from mouse and the resolution is pretty low not sure really how to do fusion of MRI with PET they are not same size. trying to put landmarks on image but I am not sure it is exactly identical place in other image. please if anyone has step by step tutorial help me crying
Hi, A litlle question, where is the HU (Hounsfield unit) in the software or in what part?, is the same rank of threshold?, thank you for the explication and help me, please.
In the bottom left, next to the letter "B" you get coordinates and current HU value in bold. Check out tutorial #8 from 2:57 for more detailed explanation. ua-cam.com/video/XiFqywwCUYA/v-deo.html
Dear everybody, is there a possibility to draw a ROI in 3D Slicer without the use of the segmentation tools? For example when you do the segmentation, but you still need a ROI for something else that is not included in the segmentation. Kind regards
You're probably looking for so called "Markups". There are regular ROIs/ruler/fiducials etc. available in Slicer: slicer.readthedocs.io/en/latest/user_guide/modules/markups.html
Hello I couldn't modify the window which is representing the data to change the contrast of the view as you said you can do it by click and dragging using the left mouse button. is there another way to do that? I'm using slicer 4.11.202
Hi, as I mentioned in the other comment, that is a new behavior that was introduced in Slicer 4.11. The video is based on Slicer 4.10. In Slicer >=4.11 that you are using, you will need to click on a brightness adjustment icon in the top bar. See this video for an example: ua-cam.com/video/u1B0F1KcVsk/v-deo.html
Hi, I'm not sure what do you mean by that? A Master Volume is a unique "image". How would you like them to be combined? Or do you mean that you want to combine two segmentations?
@@janwitowski no, every of my single Master Volumes contains 3 views (axial, sagittal, coronal), i wanted to take 1 view from each Master Volume und make a seperate Master Volume that contains 1 view from each Master Volume, example i have 3 Master Volumes (Master Volume X, Master Volume Y, Master Volume D), from Master Volume X i want to take the Axial View, from Master Volume Y the Saggital View and from Master Volume D the Coronal View and put these 3 Views in one new Master Volume S?
@@takerrazer120 So you have multiple low-resolution acquisitions in different planes and you want to make them into a one 3D volume? If yes, it's not that simple, look at the thread here: discourse.slicer.org/t/combining-volumes-what-am-i-missing/2941/2
Sorry, too little information to answer that one. You'd need to say what are the formats you're using, where does the data come from, preferably share it, etc. I think this would be better addressed on the Slicer Discourse forums.
@@JohnWick-vp5zc Ah, that is a new behavior that was introduced in Slicer 4.11. The video is based on Slicer 4.10. In Slicer >=4.11 that you are using, you will need to click on a brightness adjustment icon in the top bar. See this video for an example: ua-cam.com/video/u1B0F1KcVsk/v-deo.html
Hi! There is free sample data inside 3D Slicer. You can load it by either: (1) after starting Slicer, click on "Download Sample Data" in the left-side panel; (2) in the main menu bar at the top, click magnifying glass icon next to "Modules" and search for "Sample Data" module. Then you can choose a dataset of your choice. CTA abdomen or CTACardio would be good choices for this tutorial.
I saw all your vidéos,and i really like them, thank you very much from algeria (africa).
Thank you very much!
as you made the transition from tutorial 1, you skipped over the actual file selection, which may be 'trivial', but, where do you get the data? can you import/link from an existing database, like osirix or Horus?
now, in tutorial 2, you suddenly have data in the Dicom browser.
Thank you so much for your valuable guidance
Thank you so much for all your videos.
I wanted to ask. is there somewhere an explanation regarding on how to cut and use the slicer with an STL file extracted from solid?
Thank you so much for your efforts!😊
So nice! Very helpful!
where i can find the same picture like that? i try to find it but dont find it in internet just a single picture
Using the ruler function. How would I go about keeping it on the screen whilst scrolling through the model so I can line up other measurements with that one?
Great Video... how do u identify which segment is which part of heart or any other organ. I mean for someone who does not know where is arota or what is its location, how should they handle the situation?
Hi, honestly, it's best to find a radiologist or another expert who could teach you how to read the images and identify anatomical structures. Alternatively, you can look online for anatomical atlases.
ok, now, it would be useful to point out that you are scrolling through the series with that bar at the top of each view ... in segmentation editor, you said, click 'undo', where is it?
when first painting the aorta, it was not visible, or explained, how you moved through the slices, as you painted...
so, unlike the painting tool, threshold works in all slices, simultaneously. the 'painting-type' tools work in only one slice at a time?
Does anyone know a nifty way to fill the inside of ring (maybe a couple of rings in the stack are incomplete)? Or is there a useful tutorial for that? I have a fiber data that I would like to render. The signal intensity of its edge is bright, making it easier to segment. However, the signal intensity of inside and outside (i.e. air) of fiber is almost the same. That returns the segmentation result of a tube rather than a cylinder.
I am working with images from mouse and the resolution is pretty low not sure really how to do fusion of MRI with PET they are not same size. trying to put landmarks on image but I am not sure it is exactly identical place in other image. please if anyone has step by step tutorial help me crying
tks for what you share to community! But I can not follow all the words which you talk about, so can you send me this video's transcript? tks a lot!
hi, I just added captions to the video. You should be able to see captions as well as read the transcript now.
How to import image to 3d slicer
Hi, A litlle question, where is the HU (Hounsfield unit) in the software or in what part?, is the same rank of threshold?, thank you for the explication and help me, please.
In the bottom left, next to the letter "B" you get coordinates and current HU value in bold. Check out tutorial #8 from 2:57 for more detailed explanation. ua-cam.com/video/XiFqywwCUYA/v-deo.html
Thank you so much
Dear everybody,
is there a possibility to draw a ROI in 3D Slicer without the use of the segmentation tools? For example when you do the segmentation, but you still need a ROI for something else that is not included in the segmentation.
Kind regards
You're probably looking for so called "Markups". There are regular ROIs/ruler/fiducials etc. available in Slicer: slicer.readthedocs.io/en/latest/user_guide/modules/markups.html
Hello
I couldn't modify the window which is representing the data to change the contrast of the view as you said you can do it by click and dragging using the left mouse button. is there another way to do that? I'm using slicer 4.11.202
Hi, as I mentioned in the other comment, that is a new behavior that was introduced in Slicer 4.11. The video is based on Slicer 4.10. In Slicer >=4.11 that you are using, you will need to click on a brightness adjustment icon in the top bar. See this video for an example: ua-cam.com/video/u1B0F1KcVsk/v-deo.html
it is possible to combine 2 or more Master Volumes to 1 Master Volume?
Hi, I'm not sure what do you mean by that? A Master Volume is a unique "image". How would you like them to be combined? Or do you mean that you want to combine two segmentations?
@@janwitowski no, every of my single Master Volumes contains 3 views (axial, sagittal, coronal), i wanted to take 1 view from each Master Volume und make a seperate Master Volume that contains 1 view from each Master Volume, example i have 3 Master Volumes (Master Volume X, Master Volume Y, Master Volume D), from Master Volume X i want to take the Axial View, from Master Volume Y the Saggital View and from Master Volume D the Coronal View and put these 3 Views in one new Master Volume S?
@@takerrazer120 So you have multiple low-resolution acquisitions in different planes and you want to make them into a one 3D volume? If yes, it's not that simple, look at the thread here: discourse.slicer.org/t/combining-volumes-what-am-i-missing/2941/2
where can I find scan used in tutorial ?
Sorry, this specific exam is not publicly available.
@@janwitowski 😿
Sire, i am not able to import any dicom files. Can you help me out?
Are you getting any error message? Did you try loading by dragging and dropping files directly into 3D Slicer?
I was able to load my data in only via "add data" and the dimensions are off. Do you know how to fix the dimensions?
Sorry, too little information to answer that one. You'd need to say what are the formats you're using, where does the data come from, preferably share it, etc. I think this would be better addressed on the Slicer Discourse forums.
👍👍👍👍
Hey I’m not getting the manual opacity. Is it because of my data?
Hi, sorry, what do you mean by manual opacity? Are you saying you're trying to use the brush and don't see any effects or something else?
@@janwitowski When you left click and drag, the opacity of the scan changes. But mine doesn’t, I was wondering if it was a data proble
@@JohnWick-vp5zc Ah, that is a new behavior that was introduced in Slicer 4.11. The video is based on Slicer 4.10. In Slicer >=4.11 that you are using, you will need to click on a brightness adjustment icon in the top bar. See this video for an example: ua-cam.com/video/u1B0F1KcVsk/v-deo.html
@@janwitowski thanks a lot mate!
What is segmentation, how would you define it and why is it important to segment before using threshold
will you please send me the data ?
Hi! There is free sample data inside 3D Slicer. You can load it by either: (1) after starting Slicer, click on "Download Sample Data" in the left-side panel; (2) in the main menu bar at the top, click magnifying glass icon next to "Modules" and search for "Sample Data" module. Then you can choose a dataset of your choice. CTA abdomen or CTACardio would be good choices for this tutorial.
Please put the Arabic translation because it is so important for me and Thanks