The recon-all option is no longer working and neither is the other one. I am getting an error. 

Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help

ERROR: Flag help unrecognized.

help

Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun  3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014

For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Isaiahs-MacBook-Pro:~ IsaiahSmith$ 

On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Isaiah

recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all

should  do the trick. <input file> should be  a *single* file in the right dicom series, or a .nii file. Don't use analyze
Bruce

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

Hello Bruce, 
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?
Isaiah 

     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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