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.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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