External Email - Use Caution
Hello Kiyotaka,
Please try refreshing your copy/install of the Ubuntu 7.2.0 distribution as the packages have been updated to fix the warning below.
I think you were using the installer, so you could try the commands below to download and re-install with apt. (If you were using the tar file then just change the file name in the wget command to be freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz, expand it in the right location and skip the commands with sum, apt remove, apt install).
.... with installer ...
$ rm -f freesurfer_7.2.0_amd64.deb
$ wget https://secure-web.cisco.com/1i8WchnZn-ZDMrXexp7WlIVIxgdWjuz06xq1yUvfYcAZHMR...
$ sum freesurfer_7.2.0_amd64.deb
20191 3199044
$ sudo apt remove freesurfer
.... output deleted ....
$ apt install ./freesurfer_7.2.0_amd64.deb
.... output deleted ...
.... check environment ...
$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
.... the output should have no warnings and you can also check ...
$ env | grep MINC
MINC_BIN_DIR=/usr/local/freesurfer/7.2.0/mni/bin
MINC_LIB_DIR=/usr/local/freesurfer/7.2.0/mni/lib
$ which nu_correct
/usr/local/freesurfer/7.2.0/mni/bin/nu_correct
- R.
-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /usr/local/freesurfer/7.2.0FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined. 'nu_correct' and other MINC tools are used by some Freesurfer utilities. Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined. Some Freesurfer utilities rely on the MINC toolkit libraries. Set NO_MINC to suppress this warning.FSL_DIR /usr/local/fsl =====