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/SRS00001> -all
-bash: os005a1001.nii: No such file or directory
On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto: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.
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