Learning to use 3D Slicer

I’m an absolute beginner, and find the ‘Quick Start’, for example, not very useful, to begin, as I have no idea how the system is organised, what a ‘Module’ is, what a ‘Scene’ is, and the UI… there is a UI section, but it is way down the list, and should probably have at least a subset included before the quick start.
Without any idea of the structure of this ‘world’, and connections between its parts, the Quick Start just confuses me…
Because of my current Neuro condition, I can’t quite manage to be as constructive as I’d like to be, but there needs to be some kind of structured way to understand the system’s ‘components’, before jumping into it.
It’s super exciting to imagine what can be done, even by a rank amateur, but it’s so, so hard to get started.


Welcome to the forum and the world of 3D Slicer.
Maybe the easiest way to dive into the program is to watch one of the video tutorials.

Here is a link to the start of a good video series (give it thumbs up, referring to Slicer 4 but most of it is still valid):

In case you have questions, please search this forum for specific keywords, only in case you do not find results, start a new thread.

thanks…i had a look at the first three of the series, and made several comments, because there were several things that got skipped over, and things that ‘just happened’, without it being clear to novices… the tutorial II looks a bit different, so I’ll need to look more closely.

1 Like

My 2 cents.

Allow yourself 3 months of deep tinkering and research and don’t voice any complaint before completing the 3 months. Whenever you stumble down, don’t say ‘it should have been made easier or better’, rather, ‘I’m still missing something’. You won’t get the big picture of Slicer’s internals right way, it’s not a text editor. You will near it with constancy and patience. And you won’t ever know every part of Slicer; after 10 years, there are still zones that I don’t master (I don’t need these anyway).

As you see, help yourself with an appropriate psychological setup in front of a beast you have to tame. Slicer is a nice piece of jewellery.

1 Like

thanks for responding to my concerns … however, i have been working in a very complex environment for a long time, and have some expectations about learning curves … in viewing the ‘beginner’ tutorials, the producers are doing a tough job (I’ve had to do some of this myself), but it’s too easy to forget to point out details, and concepts, that are core to understanding the creature, when you’ve lived with it for a while. It’s a bit of a stretch to expect people who are engaged in ‘heavy’ work to spend months learning even the basics of a tool.
what i tried to do in viewing, and commenting on, the first three tutorials, is to learn, but also suggest changes, or additions, that will get someone up the curve faster… there is no ‘plus’ yo having something be more difficult than absolutely necessary.
My first click on making something 3D resulted in a black cube, and figuring out that i needed to select some preset took a while, when true to adjust brightness and contrast of the black cube was fruitless …after i tried several presets, i got a stunning 3D image, but then, the ‘shift’ control was not adaptive to that preset, and very small adjustments “blew up” the image… the segmentation editor also had me frazzled, as it wasn’t immediately obvious that it worked on only one slice at a time, and didn’t seem to do anything, well, anything obvious to me.
it’s clearly a toolbox, maybe even a tool store, but sure hard to get through the front door! :wink:
I’m a persistent kind of creature…

Thanks for sharing your experience and suggestions @Lohi, it is very helpful and we welcome your input. From your description I’m thinking you may benefit from a hands-on workshop with the chance to ask questions at every step of the way.

We have held these introductory sessions in the past but I don’t think there’s one scheduled in the near future. May I ask what time zone you are in? Now that you’ve raised the point maybe others could add their thoughts and we could arrange a zoom session for newcomers or similar as part of the upcoming project week.

I’m in CET, you know, Berlin time zone. :wink:

what i’be found, thus far, is that some relatively minor changed in tutorials and documentation can make a significant difference in learning these intrinsically-complex tools.
it’s certainly not my aim to devalue the efforts that go into all of these guides, tutorials, references, et al, just trying to add value as i work away at being minimally-functional with this mighty tool/toolbox/machine shop :slight_smile:

The challenge is Slicer changes rather quickly in matters of 12-18 months periods. It is hard to keep all the documentation up to date and correct. (workflows often doesn’t change but the way you interact with the data, or the menus may change, all which require recreating the tutorials).

Because Slicer is used in so many different settings, tutorials also tend to be specific to the modality or the workflows used by that specific community. For example, for SlicerMorph we maintain a tutorial set at GitHub - SlicerMorph/Tutorials: SlicerMorph module tutorials, but they are not going to be very useful for you, if you are not working with high-resolution microCT datasets of biological samples.

Nowadays for new people, I suggest to go through the readthedocs page carefully and then move to the specifics.

This specific issue is due to Slicer being a very generic tool. It is used for processing images of all scales and types, from microscopy images to astronomy. Your image probably comes from an uncalibrated image, such as a micro-CT, which can have very unusually narrow or unusually wide intensity range, which makes the default slider range not a good fit for your data.

It can be solved by either documenting such limitations and what to do about it, or add presets for the type of data you work with, or figure out a way of automatic adjustment of the range of these sliders. You can post separate topic on this forum about any specific issue that you encounter and we’ll help you figuring out what’s the best solution.