Hi, there,

I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. 

Following the instruction on this webpage:

http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation

I used the command 

recon-all -s my subject -all -hippo-subfields

It was running well, however, it halted/paused after it displayed the following information:"final transformation (x=..,yr=..,zr=..) and a 4x4 matrix".

For a week it is not going anywhere and not producing any output.

The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer.

Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!!

-Irene