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 $FREESURFER_HOME/subjects
Andrew
On Nov 8, 2017, at 3:51 AM, Danny Deng <dannytang023@gmail.commailto:dannytang023@gmail.com> wrote:
Hi Andrew,
I have followed your suggestion and the error pop up like this:
Xues-MacBook-Air:~ DannyDeng$ 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 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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.edumailto:AHOOPES@mgh.harvard.edu> wrote:
recon-all -i sample-001.nii.gz -s bert -all
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