Re: [Freesurfer] Questions regarding recon-all command

yes, there is no need to unzip it, we read gzipped nifti just fine Bruce On Wed, 23 Jul 2014, soumyabrata.dey wrote:

Hi Bruce,

Thanks a lot for replying.

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.

Thanks you again,

Soumya.

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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:


   o  ​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?
   o  ​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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