Dear All, 

I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I guess I will have to wait for IT to help me soon. 

Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10 [/bash]  command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause for that, though. So I might really appreciate your helps please. 

I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash. 

I found a similar discussion from the archive (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691.html) but there was no agreed solution I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems are solved?

Thank you very much for the help in advance

Kind regards

Isil