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 ${FREESURFER_HOME}/subjects recon-all -i sample-001.nii.gz -s bert -all
best, Andrew
On Nov 7, 2017, at 7:19 PM, Danny Deng <dannytang023@gmail.commailto:dannytang023@gmail.com> wrote:
Hi developers,
I just installed the software and there are so many problems I wish to seek help from you when I tried “Test your freesurfer installation” on the website
Example 2
I tried several commands as follow but all failed:
1. Xues-MacBook-Air:~ DannyDeng$ 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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