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
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