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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