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://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer_7.2.0_amd64.deb
$ 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/7.2.0
FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/username/freesurfer/7.2.0/subjects
WARNING: 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

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