does that file exist? You don't want angle brackets <> around the name (the angle brackets typically mean "replace this with an actual name"

cheers
Bruce

On Wed, 30 Jul 2014, Isaiah C. Smith wrote:

Hello and thanks again, Bruce,
I am not sure what is going wrong here. I tried what you said and I am
getting this. 

Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i <os005a1001.nii> -s
<Practice> 
-sd</Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SR
S00001> -all

-bash: os005a1001.nii: No such file or directory

On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fis...@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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