​Hi All,

I am new to freeSurfer and need your guidance for some of the doubts I have. 

I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying <filename>.hdr is not found (I have also tried with inputting .img file).

My questions are:

• ​Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option?
  
• ​Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there.
  

Thanks for your help,

Soumya.