Hi Danny,
The SUBJECTS_DIR variable defines the path to a directory where freesurfer
recon data is stored for a particular study. When setting this path variable,
you don’t need to include the <> brackets.
After sourcing freesurfer, start by making a sample directory and defining your
SUBJECTS_DIR like this:
mkdir test_subjects
export SUBJECTS_DIR=/path/to/test_subjects
then try running a sample recon:
cd ${FREESURFER_HOME}/subjects
recon-all -i sample-001.nii.gz -s bert -all
best,
Andrew
On Nov 7, 2017, at 7:19 PM, Danny Deng
<dannytang...@gmail.com<mailto:dannytang...@gmail.com>> wrote:
Hi developers,
I just installed the software and there are so many problems I wish to seek
help from you when I tried “Test your freesurfer installation” on the website
Example 2
I tried several commands as follow but all failed:
1. Xues-MacBook-Air:~ DannyDeng$ export
SUBJECTS_DIR=<$FREESURFER_HOME/subjects/sample-001.mgz .>
-bash: syntax error near unexpected token `newline’
2. Xues-MacBook-Air:~ DannyDeng$ > export SUBJECTS_DIR=<cp
$FREESURFER_HOME/subjects/sample-001.mgz .>
-bash: syntax error near unexpected token `newline’
3. Xues-MacBook-Air:~ DannyDeng$ >export
SUBJECTS_DIR=<&FREESURFER_HOME/subjects/sample-001.mgz .>
-bash: syntax error near unexpected token `newline’
4. DannyDeng$ DannyDeng$SUBJECTS_DIR
-bash: DannyDengcp/Applications/freesurfer/subjects/sample-001.mgz: No such
file or directory
Besides, I think I can’t find nifti file in my freesurfer folder.
example 3
Same problem like example 2:
Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=<cp
$FREESURFER_HOME/subjects/sample-001.mgz.>
-bash: syntax error near unexpected token `newline’
example 4: Only this one I successfully opened it.
Thanks very much.
Best Regards,
Danny Deng
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