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
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 $FREESURFER_HOME/subjects/sample-001.mgz.> -bash: syntax error near unexpected token `newline’
example 4: Only this one I successfully opened it.
Thanks very much.
Best Regards, Danny Deng
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Hi Andrew,
I have followed your suggestion and the error pop up like this:
Xues-MacBook-Air:~ DannyDeng$ 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.edu wrote:
recon-all -i sample-001.nii.gz -s bert -all
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Danny Deng -
Hoopes, Andrew