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
on behalf of Bruce Fischl
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"
mailto: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 .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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