External Email - Use Caution

Hi experts,

When I tried to gathered the volumes of hippocampus subregions from all subjects by using the commend " quantifyHAsubregions.sh", the command did not work well. There's no error message in the terminal but no file was made after that command. My data was longitudinal data, so I did the longitudinal segment used “segmentHA_T1_long.sh”. Therefore, the exact command I run for results collection was "quantifyHAsubregions.sh hippoSF T1.long subhippallvolume.txt", I also tried to provide the subject directory explicitly as fourth argument like "quantifyHAsubregions.sh hippoSF T1.long subhippallvolume.txt /media/ubuntu/cxy/FreesT1/output.long”. The results was same, there was no file.

All my subjects were pre-processed and segmentations using freesurfer version 7.1.0 on ubuntu 16.04.

I attached screenshot of my terminal window and the script of quantifyHAsubregions.sh in my computer as below.

Do you have any suggestions on how I could figure out this problem? Or other method to gather the results?

Thanks a lot!!

Molly