Hi Jasmin
you need a '-' sign first. It should be:
recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject \
joya -all &
cheers
Bruce
On Mon, 25 Jan 2016, Jasmin Alves
wrote:
Hi Bruce,
Thanks for the reply, I attempted to direct Subjects_dir to the folder with
my data but I received the following error.
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
SUBJECTS_DIR=/Desktop/Brain_Child_subs
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &
[1] 13867
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all
unrecognized.
-sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all
Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016
Thanks so much,
Jasmin
On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Jasmin
you need to create a directory where you have write permission
and room for the subject reconstruction to be written to, then
set the SUBJECTS_DIR environment variable to point to it. At the
moment you are trying to use the subject directory we
distribute, which is in some system (and read-only) location.
You can do this on the command line of recon-all via:
recon-all -sd <path to directory> ...
cheers
Bruce
On Sun, 24 Jan 2016, Jasmin Alves wrote:
Hello Freesurfer,
I am trying to learn freesurfer and ran into the following
issues below
running the recon -all command.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
1)
joya
2)
Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
T1_original_joya.nii
-subject joya -all &
3)
[1] 12300
Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
/Applications/freesurfer/subjects/joya: Permission denied
mkdir: /Applications/freesurfer/subjects/joya/scripts:
Permission denied
mkdir: /Applications/freesurfer/subjects/joya/scripts:
Permission denied
cp:
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
No such
file or directory
cat:
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
No such
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
/Applications/freesurfer/subjects/joya: No such file or
directory.
[1]+ Exit 1 recon-all -i
T1_original_joya.nii -subject
joya -a
Thank you,Jasmin
Jasmin AlvesPredoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Jasmin AlvesPredoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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