External Email - Use Caution
zhbar@DESKTOP-V43QKHC:~$ export FREESURFER_HOME=/usr/local/freesurferzhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /usr/local/freesurferFSFAST_HOME /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /usr/local/freesurfer/subjectsMNI_DIR /usr/local/freesurfer/mnizhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject datazhbar@DESKTOP-V43QKHC:~$ sudo cp $FREESURFER_HOME/subjects/sample-001.mgz .[sudo] password for zhbar:zhbar@DESKTOP-V43QKHC:~$ mri_convert sample-001.mgz sample-001.nii.gzmri_convert.bin sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from sample-001.mgz...TR=7.25, TE=3.22, TI=600.00, flip angle=7.00i_ras = (-0, -1, -0)j_ras = (-0, 0, -1)k_ras = (-1, 0, 0)writing to sample-001.nii.gz...zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject directoryzhbar@DESKTOP-V43QKHC:~$ recon-all -i sample-001.nii.gz -s bert -allERROR: SUBJECTS_DIR path does not exist.zhbar@DESKTOP-V43QKHC:~$ sudo recon-all -i sample-001.nii.gz -s bert -allsudo: recon-all: command not foundzhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)WARNING: path does not existFREESURFER_HOME /usr/local/freesurferFSFAST_HOME /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR pathMNI_DIR /usr/local/freesurfer/mni