Hi, I think that this one is for Muratmaga.
I am interested in the DeCA module, since I understood that it was able to create a template out of a series of segmented skulls, a function which would be very usefull for my researches.
Since the module code is in Github, I went to this adress GitHub - smrolfe/DeCA: Dense Correspondence Analysis (DeCA) toolkit.
I downloaded the .zip file in my download folder.
In 3DSlicer i opened the module “extensions manager” click on the folder icone (top right) from the drop menu I select the Zip file, but I got this message error. Where am I wrong?
Thanks for any help.
- the official DeCA repository is GitHub - SlicerMorph/SlicerDenseCorrespondenceAnalysis: Dense Correspondence Analysis for Surfaces (the one you linked is a development fork).
- You are using an outdated version of Slicer (5.0.2)
Install the latest stable or preview, and DeCA will be in the extension catalogue (though search for the full extension name DenseCorrespondenceAnalysis).
@lassoan when are you guys planning to improve the search functionality in the extension catalogue to search for all the keywords?
Great, I am on a trip abroad with my old laptop but, now I am eager to be back home to run the module and create the templates which are an old dream !
Envoyé de mon iPhone
This would need changing of the extensions manager frontend, so a task best suited for @jcfr. I haven’t found an open issue for this. To put it on @jcfr’s roadmap, the best would be to add an issue to slicer-extensions-webapp repository. Maybe it is not difficult to implement this, but he may have many other priorities.
OK I opened a thread Improve search capabilities for extensions · Issue #198 · KitwareMedical/slicer-extensions-webapp · GitHub
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Good morning, back home, I installed the DeCA module. I can’t find help on this module.
I understand that I need to create directories for models, landmarks and DeCA outputs.
How I name the files to do models and landmarks corresponding? etc…
Thank for help.
Make sure you are using the latest stable or the preview. If you are using the stable, do check whether you have the latest DeCA. We have revamped the UI couple months back, and now all you have to point out is where the data sits. Folder structure of the output and downstream work is now handled by the module itself.
See the latest tutorials:
Tutorials/DeCA_1 at main · SlicerMorph/Tutorials · GitHub (general shape analysis with optional asymmetry analysis).
Tutorials/DeCA_2 at main · SlicerMorph/Tutorials · GitHub (asymmetry specific workflow)
Tutorials/DeCAL at main · SlicerMorph/Tutorials · GitHub (automated dense semilandmarking with DecA)
DenseCorrespondenceAnalysis extension currently has a build failure for latest Slicer preview following the update to Python 3.12. See the following:
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Thanks for reporting. We will check.
Thank you so much for this wonderful tool.
I got my first human skull template which is very effective for the study of craniofacial malformations
Envoyé de mon iPhone
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If you are working with CT images (as opposed to surface scans), you might want to try the template building in our SlicerANTsPy. This will allow you to build a volumetric template from the CT scans. You can optionally allow for initial LM based rigid initialization.
It is in a rough (from documentation point of view), but usable state: GitHub - SlicerMorph/SlicerANTsPy: module and GUI for antspy
Hi, SlicerANTSpy looks great, but it lacks a manual for non-geeks like me.
philippe pellerin
philippepellerin@me.com
There is not much to it really. Choose a folder of NRRD, and if you have landmarks choose a folder of LMs (again this is optional and only needed if you want to do a LM based rigid initialization).
Then choose the SyNQuick as the registration and probably do at least 3 iterations…
Hi, I have created a set of 19 Skull Atlas templates from 184 normal CT scans, ranging from birth to 76 years old, using the DeCA module.I am very happy with it and would be happy to share it with anyone interested (upon request). I would like, as suggested by Murat Maga, to try the SlicerANTSpy, I downloaded it on the 5.9-2025-09-11 ,but I can’t find it among the modules menu. What is the problem? When I open the extensions display, SlicerANTSpy is visible but it does not appear in the extensions’ menu and the extension research can’t find it…
philippe pellerin
philippepellerin@me.com
2025
Extensions may not be available for every version of the preview releases for various reasons. As far as I can tell, it is available for a recent preview release (r33931). Follow this link to download that version of Slicer and try installing and using ANTsPy
I downloaded the r33931 and installed the SlicerANTsPY, but I can’t find the extension in the module menu. I am working with MacOS Sequoia 15.6
philippe pellerin
philippepellerin@me.com
You mean after you install SlicerANTsPy and restarted slicer, if you do search for ants (CTRL+F), it doesn’t show? What is in the SlicerMorph sub menu?
Can you share a full log?
Yes, I did that: downloaded r33931, then after SlicerANTsPY, restarted. I can’t see SlicerANTsPY in the menu, nor in any sub-menu, but as you can see in the screen grab, there is a folder somewhere with this name…SlicerANTsPY never came up in the menu and submenu.
Thank for your help. Best regards
P.S. It is another topic, when building up my set of skull emplates with DeCA I had an issue with the Skull Atlas 1155-1355d. The result obtained through the analysis of 11 models and markups was incoherent. I redid it several times, I checked for an error in the models and markups, and could not find any explanation. When checking the landmarks with GPA I found a model named PCA Warped Volume, which looks good as a mean statistical model.
philippe pellerin
philippepellerin@me.com
Thats the one. Everything in Antspy is registration based
I can’t see how to create a mean statistical volume with the tools available under the name ANTs
philippe pellerin
philippepellerin@me.com