How to use MBIS for brain tissue segmentation

#1

Hi, I have successfully installed the MBIS software according to the author’s github websit, https://github.com/oesteban/MBIS/wiki/Installation. However, I still don’t know how to use it. I type “–help” on the terminal and obtation some option informations, but there is no option indicate the input path of the data.


Is there anyone who could give me an example on how to use this package.

#2

Dear @xgt, the input data is provided with the -C option. For instance, if you have two nifti files, one with a T1-weighted image and a second with a T2-weighted image:
-C T1w.nii.gz T2w.nii.gz

#3

Hi,

I am trying to use MBIS with docker, using command:

docker run -ti --rm
-v /Users/dima/Desktop/sub-MU004:/Users/dima/Desktop/sub-MU004
oesteban/mbis
-C /Users/dima/Desktop/sub-MU004/sub-MU004_ses-06_space-template_desc-norm_T2star.nii.gz
/Users/dima/Desktop/sub-MU004/sub-MU004_ses-06_space-template_desc-norm_SWI.nii.gz
–out segmented
–output-stats
–segments
–class 5

the segmentation seems to work:

but I dont get any output and there is no flag for specifying the output folder

Does anybody have any idea where the results are stored?

Thank you very much!

Cheers,

Dima