External Email - Use Caution
Hello Zainab, The first 2 commands you list are, export FREESURFER_HOME=/usr/local/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.sh .... and the output from the source command shows you what has been setup in your environment... FREESURFER_HOME /usr/local/freesurferFSFAST_HOME /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /usr/local/freesurfer/subjectsMNI_DIR /usr/local/freesurfer/mni Now there should be no need to run more export commands, i.e., SUBJECTS_DIR is already set correctly. But the next export command you type, export SUBJECTS_DIR=path to subject directory - changed the setting of SUBJECTS_DIR from "/usr/local/freesurfer/subjects" to "path to subject directory" which is a path that does not exist
You only need to run the export and source commands once in your current shell before runningany/all subsequent freesurfer commands.
Zainab Albar November 7, 2018 at 19:29 External Email - Use Caution Hello Freesurfer expert, I am brand new to Freesurfer, my apology for the basic question, I kept trying to figure out my mistake in installation for last week and could not find a solution to it. Here is my output, my problem with subject_DIR keeps changing and recon command is not found. it worked only once with me till I reach example 4 when I had an output that libpng12.so.0 not found. Thank you for help in advance, zhbar@DESKTOP-V43QKHC:~$ 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer