Your cp command failed. You'll need somethin glike
cp $FREESURFER_HOME/subjects/sample-001.mgz sample-001.mgz
On 05/09/2018 12:45 AM, subin oh wrote:
Hello, Freesurfer Developer when I run the 'Test your FreeSurfer Installation' command (Example1~Example3)(https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)
I got the following errors pop up like this: Sorry for I'm a beginner.. Thanks very much for any suggestions! Best Regards, Subin Oh -------------------------[Example1~Example2]--------------------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/ FSFAST_HOME /Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer//subjects MNI_DIR /Applications/freesurfer//mni FSL_DIR /usr/local/fsl bash-3.2$ export c bash-3.2$ export SUBJECTS_DIR=/Application/freesurfer/subjects/subj01 bash-3.2$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directoy bash-3.2$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/chan/sample-001.mgz, -1): could not open file bash-3.2$ mri_convert sample-001.mgz fsample-001.nii.gz mri_convert sample-001.mgz fsample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/chan/sample-001.mgz, -1): could not open file bash-3.2$ mri_convert sample-001.mgz fsample-001.nii.gz mri_convert sample-001.mgz fsample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/chan/sample-001.mgz, -1): could not open file bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/subj01 bash-3.2$ recon-all -i sample-001.nii.gz -s subj01 -all ERROR: cannot find sample-001.nii.gz Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed May 9 12:43:41 KST 2018
For more details, see the log file To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
bash-3.2$ recon-all -i fsample-001.nii.gz -s subj01 -all ERROR: cannot find fsample-001.nii.gz Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed May 9 12:43:50 KST 2018
For more details, see the log file To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-------------------------------[Example3]------------------------ bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/ bash-3.2$ recon-all -s subj01 -all Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# MotionCor Wed May 9 12:56:55 KST 2018 ERROR: no run data found in /Applications/freesurfer/subjects/subj01/mri. Make sure to have a volume called 001.mgz in /Applications/freesurfer/subjects/subj01/mri/orig. If you have a second run of data call it 002.mgz, etc. See also:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
recon-all -s subj01 exited with ERRORS at Wed May 9 12:56:55 KST 2018
For more details, see the log file /Applications/freesurfer/subjects/subj01/scripts/recon-all.log To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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