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/freesurfer zhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject data zhbar@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.gz mri_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=7.00 i_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 directory zhbar@DESKTOP-V43QKHC:~$ recon-all -i sample-001.nii.gz -s bert -all ERROR: SUBJECTS_DIR path does not exist. zhbar@DESKTOP-V43QKHC:~$ sudo recon-all -i sample-001.nii.gz -s bert -all sudo: recon-all: command not found zhbar@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 exist FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR path MNI_DIR /usr/local/freesurfer/mni
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