The original data comes in .nii.gz format but when I unzipped it it become .hdr-.img (2 files). The freeSurfer is not understanding the .hdr-.img format but I am able to run it using .nii.gz format.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Wednesday, July 23, 2014 2:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Questions regarding recon-all command

Hi Soumya

Can you include the full command and screen output of what you ran? Are you sure that they are nifti and not analyze? Analyze is to be avoided as it doesn't contain enough information to tell left from right

Cheers

Bruce

On Jul 22, 2014, at 8:01 PM, "soumyabrata.dey" <soumyabrata.dey@knights.ucf.edu> wrote:

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.

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