NITRC iBEAT Forum: open-discussion

can ibeat be used to calculate the cortical thickness of neonate/infant brain

Yuanchao Zhang — Wed, 19 Sep 2018 9:54:08 GMT

Dear, experts

I have a cohort of neonate brain images (t1 and t2) and I want to calculate the cortical thickness. Can ibeat be used to calculate the cortical thickness of neonate/infant brain? where can I download the latest version of ibeat? is cortical thickness map integrated in the newer version? Could you send a link of the latest version?

Yuanchao

issue with installing ibeat on Centos 7

Dan Wu — Fri, 14 Sep 2018 11:23:25 GMT

Dear ibeat developers,

I am trying to install ibeat on my centos 7 system, and I have installed libXp.so.6 and Matlab MCR (v717, oldest version that I can find) as instructed. However, I still cannot run ibeat. The error message is
An Error has occurred while trying to initialize the MCR.
The error is: Fatal error loading library /home/zju/ibeat/MCR/v715/bin/glnxa64/libmwmclmcr.so Error:libXp.so.6: cannot open shared object file: No such file or directory
Error: mclmcr initialization failed.

I appreciate your help on this.

Thanks,
Dan

Automated bone segmentation from dental CBCT images using patch-based sparse representation and convex optimization

George Chao — Sun, 11 Feb 2018 4:25:35 GMT

hi does anyone have the software for this?
thanks

New Python Version

Qian Zhang — Thu, 11 Jan 2018 21:29:07 GMT

We are working on a new version with Python, Tkinter and SimpleITK so we can get rid of MATLAB.
[img]https://github.com/qzane/PyiBEAT/raw/master/iBeat_demo1.png[/img]

R: What are the features of the new version ?

Li Wang — Mon, 02 Oct 2017 21:51:07 GMT

[i]Originally posted by Jiawei Chen:[/i][quote]What are the features of the new version of iBEAT compare with the previous version?[/quote]
[color=#000000]The new version will include cross-platform interoperability (e.g., Windows, Linux, and Mac OS X).
Specifically, for infant segmentation module, beside the sparse patch-based level sets method, LINKS, topology guided fully convolutional networks will be also included, which will allow users more freedom to use their own data for training and classification to overcome the artifacts such as motion. New modules, such as surface-based analysis, will also be included.[/color]

In addition, infant voluemetric atlases and cortical surface atlases will be also released soon.

What are the features of the new version ?

Jiawei Chen — Sun, 01 Oct 2017 19:36:19 GMT

What are the features of the new version of iBEAT compare with the previous version?

RE: Infant cortical surface atlas is coming!

Li Wang — Sat, 30 Sep 2017 19:23:26 GMT

[i]Originally posted by lgn_njust:[/i][quote]Will the infant brain atlases be publicly avaiable, espcially for the 6 months of age?[/quote][color=#000000]Yes, we will provide atlases for 2 weeks, 3, 6, 9, 12, 18, and 24 months.
[/color]

RE: Infant cortical surface atlas is coming!

Li Wang — Sat, 30 Sep 2017 19:22:13 GMT

[i]Originally posted by jieyu zhang:[/i][quote]What do you think of deep learning ? In addtion to deep learning, what other ways to segment the brains?[/quote][color=#000000]Thanks for very much for your questions.[/color]

[color=#000000]There are many methods for segmentation, e.g., multi-atlas based label fusion, LINKS (https://www.ncbi.nlm.nih.gov/pubmed/25541188).[/color]
[color=#000000]Recently, deep learning based methods, e.g., ResNet, Densenet, SegNet, have achieved state-of-the-arts performance in many applications.[/color]
[color=#000000]Therefore, we will employ these deep learning based methods in the new version.
[/color]

RE: new version

Li Wang — Sat, 30 Sep 2017 19:18:07 GMT

These are great suggestioins.

We will label the infant brain images into more detailed ROIs, besides thoese WM, GM and CSF.

Thanks.

RE: Infant cortical surface atlas is coming!

lgn_njust — Sat, 30 Sep 2017 2:38:41 GMT

Will the infant brain atlases be publicly avaiable, espcially for the 6 months of age?