Before I dive into understanding all of your code I wanted to check if
either you can point me in the right direction, I am on a really tight
deadline that I might only be able to meet if I go straight to the
solution.



I am trying to do shape analysis of the skull across babies aged 0-12
months. I have been trying to use ShapeWorksGroom but the software
complaints because there is different image supports for the different
bone-labeled head volumes. My images have different sizes, and are not
aligned to each other. Is there an easy way to have the code do the
magic for me without having to go into much detail?


One first difficulty I found is that when I apply the center command in ShapeWorksGroom the result is an all-zero volume. Any ideas?


Thank you indeed.

Best,



Carlos S. Mendoza, Ph.D.

Postdoctoral Fellow

Sheikh Zayed Institute for Pediatric Surgical Innovation

Children's National Medical Center

111 Michigan Avenue, NW

Washington, DC 20010

Phone: 202-476-1272

E-mail: [url=mailto:CMendoza@cnmc.org]CMendoza@cnmc.org[/url], [url=mailto:carlos.sanchez.mendoza@gmail.com]carlos.sanchez.mendoza@gmail.com[/url]

Hi Carlos

Apologies for the delay in responding to your query.

There are some limitations to ShapeWorks in terms of the data it can handle.
One of them is that it expects the input binary segmentations to have a common label value (which can be specified in the parameter file as the foreground_value). It would be best if you can pass your segmentations through a thresholding pipeline to get such an ensemble. I suspect that you get all-zero volumes upon centering due to the same reason (i.e. multiple foreground values)
ShapeWorks also expects the input segmentations to be "roughly aligned" and a tool for rigid alignment is provided in the 'Unsupported' section of the build. This tool is called 'alignshapes' and allows for pairwise rigid alignment of shapes. If the size of your ensemble is not very large, perhaps this tool can help with pairwise initial alignment to a common reference segmentation. The command line for this tool is: alignshapes ref_segmentation mov_segmentation
To get images of the same size, you could try the 'auto_pad' option with ShapeWorksGroom. If this does not work in a satisfactory manner, please let me know and i can share some other tools to help with this.

Hope this answers your questions... and is still of some help :)
Regards
manasi