Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right?

Hi Isaiah,

what are the input images that you have? What format and what imaging
sequence? You should be able to just run recon-all on them (check out
recon-all -help)

cheers
Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:

Hello All,

I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.

Isaiah Smith
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