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 =====
External Email - Use Caution
Dear R,
Thank you very much! I followed your instructions, and it worked perfectly.
Best regards,
Kiyotaka
On Thu, Jul 22, 2021 at 3:20 AM fsbuild fsbuild@contbay.com wrote:
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/1FK_sXs4RH2RQpXvxlC81vWqvKNznb76Y5pxgR_orSVStzm... $ 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 =====
External Email - Use Caution
Hi,
On 7/21/21 8:20 PM, fsbuild wrote:
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 just found this post and it explains why I'm seeing this:
$ ls -lrt freesurfer-linux-centos6_x86_64-7.2.0.tar.gz* -rw-r--r-- 1 krause domain users 4917297770 Jul 15 13:05 freesurfer-linux-centos6_x86_64-7.2.0.tar.gz -rw-r--r-- 1 krause domain users 5012301197 Jul 21 08:13 freesurfer-linux-centos6_x86_64-7.2.0.tar.gz.1
$ md5sum freesurfer-linux-centos6_x86_64-7.2.0.tar.gz* cac0f97a4034c3c234fdbe99707d7d93 freesurfer-linux-centos6_x86_64-7.2.0.tar.gz eae2d09b063794bf2c8ed3e50ee80bd8 freesurfer-linux-centos6_x86_64-7.2.0.tar.gz.1
$ tar tf freesurfer-linux-centos6_x86_64-7.2.0.tar.gz.1 freesurfer/mni/bin/mritotal freesurfer/mni/bin/mritotal $ tar tf freesurfer-linux-centos6_x86_64-7.2.0.tar.gz freesurfer/mni/bin/mritotal tar: freesurfer/mni/bin/mritotal: Not found in archive tar: Exiting with failure status due to previous errors
Can I say that, as a sysadmin / package maintainer, I find this a little unfortunate. There is no way for me to know that I had to get a new tar ball, because the version number stayed exactly the same :( It's just that I found this post *after* we stumbled over an issue with the missing MNI directory.
best regards Michael
freesurfer@nmr.mgh.harvard.edu