Ubuntu: Problems with testing FreeSurfer Installation



Question:

I have followed the instructions from:
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/
I have tested whether FreeSurfer worked properly from the site: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#TestyourFreeSurferInstallation
However, I've encountered some problems at step 2. Did the freesurfer properly installed? I have no way to see whether I can properly use it and track the results using freeview. I don't know why such error (below) occurred.

eternal@DESKTOP-UNTM4IS:~$ recon-all -i sample-001.nii.gz -s bert -all  ERROR: You are trying to re-run an existing subject with (possibly)    new input data (-i). If this is truly new input data, you should delete    the subject folder and re-run, or specify a different subject name.    If you are just continuing an analysis of an existing subject, then    omit all -i flags.  

Below are the 'bash' and lists of items for each directory. I think something is wrong in the line 2 (no such file or directory). The same command output is displayed three times. Is it a problem? If it is, how can I correct it and how can I modify the bash codes?

eternal@DESKTOP-UNTM4IS:~$ bash  bash: /usr/local/freesurfer=/SetUpFreeSurfer.sh: no such file or directory  -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------  Setting up environment for FreeSurfer/FS-FAST (and FSL)  FREESURFER_HOME /usr/local/freesurfer  FSFAST_HOME /usr/local/freesurfer/fsfast  FSF_OUTPUT_FORMAT nii.gz  SUBJECTS_DIR /usr/local/freesurfer/subjects  MNI_DIR /usr/local/freesurfer/mni  FSL_DIR /usr/share/fsl/5.0  -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------  Setting up environment for FreeSurfer/FS-FAST (and FSL)  FREESURFER_HOME /usr/local/freesurfer  FSFAST_HOME /usr/local/freesurfer/fsfast  FSF_OUTPUT_FORMAT nii.gz  SUBJECTS_DIR /usr/local/freesurfer/subjects  MNI_DIR /usr/local/freesurfer/mni  FSL_DIR /usr/share/fsl/5.0  -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------  Setting up environment for FreeSurfer/FS-FAST (and FSL)  FREESURFER_HOME /usr/local/freesurfer  FSFAST_HOME /usr/local/freesurfer/fsfast  FSF_OUTPUT_FORMAT nii.gz  SUBJECTS_DIR /usr/local/freesurfer/subjects  MNI_DIR /usr/local/freesurfer/mni  FSL_DIR /usr/share/fsl/5.0    eternal@DESKTOP-UNTM4IS:~$ ls  bashrc   freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz   matlab     sample-001.mgz   sample-001.nii.gz    eternal@DESKTOP-UNTM4IS:/usr/local/freesurfer$ ls  ASegStatsLUT.txt     NOTICE     WMParcStatsLUT.txt   fsafd      sources.csh  AUTHORS              README     average              fsfast     sources.sh  DefectLUT.txt        SegmentNoLUT.txt                bin        lib  subjects             FreeSurferColorLUT.txt          SetPuFreeSurfer.csh  build-stamp.txt      license.txt                     tkmeditParcColorsCMA  FreeSurferEnv.csh    SetUpFreeSurfer.sh              data       matlab  tktools              FreeSurferEnv.sh  Simple_surface_labels2009.txt   diffusion            mni        trctrain  LICENSE              VERSION    docs                 sessions    eternal@DESKTOP-UNTM4IS:/usr/local/freesurfer/subjects$ ls  README bert     cvs_avg35-inMNI152   fsaverage3       fsaverage5  fsaverage_sym   rh.EC_average        sample-002.mgz   V1_average  cvs_avg35       fsaverage3           fsaverage4       fsaverage6  Ih.EC_average   sample-001.mgz  

Thanks for reading!


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