When setting SUBJECTS_DIR, you have to specify the actual path to the “test_subjects” directory that you created. "/path/to/test_subjects" isn’t a real path on your computer. In your case, the path might be something like "/Users/DannyDeng/test_subjects”

In recon-all, the -i flag is used to designate the path to an input volume. In example 1, sample-001.mgz is converted to sample-001.nii.gz . My guess is you haven’t done this step, because freesurfer “cannot find sample-001.nii.gz”. Try using “-i  sample-001.mgz” instead, as this file is included in the freesurfer distribution under $FREESURFER_HOME/subjects

Andrew

On Nov 8, 2017, at 3:51 AM, Danny Deng <dannytang023@gmail.com> wrote:

Hi Andrew,

I have followed your suggestion and the error pop up like this:

Xues-MacBook-Air:~ DannyDeng$ mkdir test_subjects
mkdir: test_subjects: File exists
Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=/path/to/test_subjects
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects/sample-001.nii.gz
-bash: cd/Applications/freesurfer/subjects/sample-001.nii.gz: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects
-bash: cd/Applications/freesurfer/subjects: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd ${FREESURFER_HOME}/subjects
Xues-MacBook-Air:subjects DannyDeng$ recon-all -i sample-001.nii.gz -s bert -all
ERROR: cannot find sample-001.nii.gz
Darwin Xues-MacBook-Air.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Wed Nov  8 16:50:37 HKT 2017

For more details, see the log file 

Xues-MacBook-Air:subjects DannyDeng$ 

Sorry I am a beginner.

Best Regards,
Danny Deng

On Nov 8, 2017, at 10:48 AM, Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

recon-all -i sample-001.nii.gz -s bert -all


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