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Hello,

Please see the following installation I attempted.

banikr2@banikr:~$ which yum

I already had a previous faulty freesurfer installed.

banikr2@banikr:~$ ls -l -h

drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer
-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz

For some reason, the freesurfer directory had only 4Kb size.

banikr2@banikr:~$ rm -rf freesurfer
banikr2@banikr:~$ ls -l -h

-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz

banikr2@banikr:~$ cd $HOME
banikr2@banikr:~$ sum freesurfer-linux-centos6_x86_64-7.1.1.tar.gz 
55852 4560006

banikr2@banikr:~$ tar zxpf freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
banikr2@banikr:~$ ls -l -h

drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer
-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz

banikr2@banikr:~$ ls freesurfer
ASegStatsLUT.txt  DefectLUT.txt  FreeSurferColorLUT.txt  fsfast  python               SetUpFreeSurfer.sh             subjects              WMParcStatsLUT.txt
average           diffusion      FreeSurferEnv.csh       lib     SegmentNoLUT.txt     Simple_surface_labels2009.txt  tkmeditParcColorsCMA
bin               docs           FreeSurferEnv.sh        matlab  sessions             sources.csh                    tktools
build-stamp.txt   etc            fsafd                   mni     SetUpFreeSurfer.csh  sources.sh                     trctrain
banikr2@banikr:~$ export FREESURFER_HOME=$HOME/freesurfer
banikr2@banikr:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /usr/local/freesurfer/fsfast does not exist
FREESURFER_HOME   /home/banikr2/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/banikr2/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
WARNING: MINC_BIN_DIR '/usr/local/freesurfer/mni/bin' does not exist.
WARNING: MINC_LIB_DIR '/usr/local/freesurfer/mni/lib' does not exist.
FSL_DIR           /usr/local/fsl

banikr2@banikr:~$ ls -l -h
drwxrwsr-x 17 banikr2 banikr2  4.0K Jul 23  2020  freesurfer
-rwxrwxrwx  1 banikr2 banikr2  4.4G Sep 24 13:17  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
The same error persists.

Rana Banik

From: fsbuild <fsbuild@contbay.com>
Sent: Saturday, September 25, 2021 8:23 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Banik, Rana <rana.banik@vanderbilt.edu>
Subject: Re: [Freesurfer] Freesurfer installation error?

It looks like you want to install and run the 7.1.1 release on CentOS6.

The fsfast and mni subdirectories are in the distribution, so I am not sure why you are getting that output. I suggest trying to do a clean install from scratch. There are a couple of ways to do that, i.e., clean install under /usr/local and-or clean install under your home ($HOME) directory. I will list instructions for both.

If you already installed under /usr/local, then you should have sudo/admin privileges to write files there. A simple way to check that is to try and run a harmless command with sudo, e.g.,

$ sudo date

[sudo] password for <your userid>: <—— enter your password

If your password is accepted then the date command will run and print out the date. If not, it will ask you to enter a password again. If your password does not work then it means you do not have sudo privileges and you won't be able to run the installer. In that case, hit Ctrl-C to get out of the password prompt and go to INSTALL IN HOME DIRECTORY below. You should not need any special privileges to write or delete files on your home directory.

CLEAN INSTALL IN /USR/LOCAL

Only try this if sudo/admin privileges worked above for the command “sudo date”.

First make sure you have the “yum” command installed,

$ which yum

/usr/bin/yum

If you don’t have the yum package manager command installed, then stop and go to the instructions for INSTALL IN HOME DIRECTORY.

If you do have the yum command, then make sure you can download the CentOS6 installer. You can download this directly into your home directory from the terminal,

$ cd $HOME

… get the 7.1.1 installer for CentOS6 … if wget does not work or you don’t have that command you can use that link in your browser to download it ...

$ wget MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-CentOS6-7.1.1-1.x86_64.rpm

… wait for the download to finish via its progress bar and then check you have the complete installer file ....

$ sum freesurfer-CentOS6-7.1.1-1.x86_64.rpm

53407 3836829

If you did not get those exact numbers from the output of the checksum command, then re-try your download until you get that result. If you can’t get the download to work then go to instruction for INSTALL IN HOME DIRECTORY.

If the download worked, then remove any existing freesurfer installation under /usr/local

$ cd /usr/local

$ ls

If you do not see a freesurfer subdirectory then skip the next 2 commands (chmod and rm) and proceed to running the installer,

$ sudo chmod -R 777 freesurfer

$ sudo rm -rf freesurfer

Now ls and make sure no freesurfer directory is there,

$ ls

Now try running the installer from your home directory,

$ cd $HOME

$ sudo yum —nogpgcheck localinstall freesurfer-CentOS6-7.1.1-1.x86_64.rpm

… answer y (for yes) to any questions and wait for the install to finish …

Now do an ls of the new installation,

$ ls /usr/local/freesurfer/7.1.1-1

… and you should see both an fsfast and mni subdirectory there..

Try setting the environment again but with FREESURFER_HOME set to the new install path,

$ export FREESURFER_HOME=/usr/local/freesurfer/7.1.1-1

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

CLEAN INSTALL IN HOME DIRECTORY

This should work no matter what is or is not installed under /usr/local.

Go to your home directory (always set as the value of the environment variable HOME)

$ cd $HOME

… get the 7.1.1 tar archive for CentOS6 … if wget does not work or you don’t have that command you can use that link in your browser to download it ...

… wait for the download to finish via its progress bar and then check you have the complete archive file ...

$ sum freesurfer-linux-centos6_x86_64-7.1.1.tar.gz

55852 4560006

If you did not get those exact numbers from the output of the checksum command, then re-try your download until you get that result.

If the download worked, then remove any existing freesurfer installation

$ ls

If you do not see a freesurfer subdirectory then skip the “rm” command

$ rm -rf freesurfer

Now unarchive the tar archive with,

$ tar zxpf freesurfer-linux-centos6_x86_64-7.1.1.tar.gz

You should now have a ./freesufer directory under $HOME. With ls command you should see the fsfast and mni subdirectories there,

$ ls freesurfer

Try setting the environment again but with FREESURFER_HOME set to ./freesurfer under your HOME directory. (Note there is no subdirectory with a version number when using the tar archive).

$ export FREESURFER_HOME=$HOME/freesurfer

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

- R.

On Sep 25, 2021, at 12:39, Banik, Rana <rana.banik@vanderbilt.edu> wrote:
External Email - Use Caution

External Email - Use Caution
Installed freesurfer with the following errors. 
banikr2@banikr:~/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /usr/local/freesurfer/fsfast does not exist
FREESURFER_HOME   /home/banikr2/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/banikr2/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
WARNING: MINC_BIN_DIR '/usr/local/freesurfer/mni/bin' does not exist.
WARNING: MINC_LIB_DIR '/usr/local/freesurfer/mni/lib' does not exist.
FSL_DIR           /usr/local/fsl
I can run freeview with the following:
banikr2@banikr:~/freesurfer$ freeview
Is the installation done correctly? Do the warnings compromise anything?

Rana Banik
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