The command is not found.
Last login: Tue Jul 29 17:42:52 on ttys001
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i os005a1001.nii -s Practice -sd
/Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SRS00001
-all
-bash: recon-: command not found
Isaiahs-MacBook-Pro:~ IsaiahSmith$ -bash: os005a1001.nii: No such file or
directory
On Jul 22, 2014, at 4:44 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu<mailto: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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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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