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.
____________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
<fis...@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....@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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