External Email - Use Caution
You need to install the tcsh shell:
sudo apt-get install tcsh
Best,
Tim
On October 3, 2019 at 6:30 PM Tim Schäfer tim@rcmd.org wrote:
You need to install the tcsh shell:
sudo apt-get install tcsh
Best,
Tim
On October 3, 2019 at 6:26 PM Theotonio Pauliquevis theotonio@gmail.com wrote:
External Email - Use CautionHi,
I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical (and strange) problem in the earlier tests of freesurfer (Example 2). Any help would be appreciated. Basically, when trying example 2 in instructions homepage I got the following error:
theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory
But the fact is that recon-all is there and apparently it is well configured, because 1) the recon-all does exist, and 2) permissions are ok:
theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all -rwxrwxr-x 1 8481 1590 327555 Jan 18 2017 /usr/local/freesurfer/bin/recon-all
and the command is promptly recognized :
theo@theo-Inspiron-5457:~$ which recon-all /usr/local/freesurfer/bin/recon-all/
Any ideas? Anybody got this issue before? It seems to be some (not obvious) permission problem.
Below I type the whole procedure to install, so one can see that I followed all installation instructions.
History:
Successfully downloaded and unzipped the files at /usr/loca/freesurfer
Successful set up of environment variables after including the following
lines in .bashrc:
############################################## #Software FREESURFER - Enviroment variables # export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/theo/freesurfer/subjects ##############################################
BTW, "theo" is my userID
File license.txt copied to /usr/local/freesurfer
message after open a terminal window confirms that Enviroment variables
were correctly set:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni (base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR /home/theo/freesurfer/subjects (base) theo@theo-Inspiron-5457:~$
Any help is welcome Regards
Theotonio _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
External Email - Use Caution
Hi,
Thanks for the prompt reply.
After I installed tcsh it did run successfully.
Since this fixing I did run example 2, and it is still running, continuously, during the last 3h25min.
Is that normal?
Attached it is my screen output in case someone could see any problems in my (intermediary) results.
BTW, it is still running while I write this e-mail to the group.
Regards
Theotonio
Em qui, 3 de out de 2019 às 13:32, Tim Schäfer ts+ml@rcmd.org escreveu:
External Email - Use CautionYou need to install the tcsh shell:
sudo apt-get install tcsh
Best,
Tim
On October 3, 2019 at 6:30 PM Tim Schäfer tim@rcmd.org wrote:
You need to install the tcsh shell:
sudo apt-get install tcsh
Best,
Tim
On October 3, 2019 at 6:26 PM Theotonio Pauliquevis <
theotonio@gmail.com> wrote:
External Email - Use CautionHi,
I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical (and strange) problem in the earlier tests of freesurfer (Example 2).
Any
help would be appreciated. Basically, when trying example 2 in
instructions
homepage I got the following error:
theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter:
No
such file or directory
But the fact is that recon-all is there and apparently it is well configured, because 1) the recon-all does exist, and 2) permissions
are ok:
theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all -rwxrwxr-x 1 8481 1590 327555 Jan 18 2017 /usr/local/freesurfer/bin/recon-all
and the command is promptly recognized :
theo@theo-Inspiron-5457:~$ which recon-all /usr/local/freesurfer/bin/recon-all/
Any ideas? Anybody got this issue before? It seems to be some (not
obvious)
permission problem.
Below I type the whole procedure to install, so one can see that I
followed
all installation instructions.
History:
- Successfully downloaded and unzipped the files at
/usr/loca/freesurfer
- Successful set up of environment variables after including the
following
lines in .bashrc:
############################################## #Software FREESURFER - Enviroment variables # export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/theo/freesurfer/subjects ##############################################
BTW, "theo" is my userID
File license.txt copied to /usr/local/freesurfer
message after open a terminal window confirms that Enviroment
variables
were correctly set:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni (base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR /home/theo/freesurfer/subjects (base) theo@theo-Inspiron-5457:~$
Any help is welcome Regards
Theotonio _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, depending on your hardware it can take >12 hours, particularly if you aren't using -openmp On Thu, 3 Oct 2019, Theotonio Pauliquevis wrote:
External Email - Use Caution
Hi, Thanks for the prompt reply.
After I installed tcsh it did run successfully.
Since this fixing I did run example 2, and it is still running, continuously, during the last 3h25min.
Is that normal?
Attached it is my screen output in case someone could see any problems in my (intermediary) results.
BTW, it is still running while I write this e-mail to the group.
Regards
Theotonio
Em qui, 3 de out de 2019 às 13:32, Tim Schäfer ts+ml@rcmd.org escreveu: External Email - Use Caution
You need to install the tcsh shell: sudo apt-get install tcsh Best, Tim > On October 3, 2019 at 6:30 PM Tim Schäfer <tim@rcmd.org> wrote: > > > You need to install the tcsh shell: > > sudo apt-get install tcsh > > Best, > > Tim > > > On October 3, 2019 at 6:26 PM Theotonio Pauliquevis <theotonio@gmail.com> wrote: > > > > > > External Email - Use Caution > > > > Hi, > > > > I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical > > (and strange) problem in the earlier tests of freesurfer (Example 2). Any > > help would be appreciated. Basically, when trying example 2 in instructions > > homepage I got the following error: > > > > theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all > > bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No > > such file or directory > > > > But the fact is that recon-all is there and apparently it is well > > configured, because 1) the recon-all does exist, and 2) permissions are ok: > > > > theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all > > -rwxrwxr-x 1 8481 1590 327555 Jan 18 2017 > > /usr/local/freesurfer/bin/recon-all > > > > and the command is promptly recognized : > > > > theo@theo-Inspiron-5457:~$ which recon-all > > /usr/local/freesurfer/bin/recon-all/ > > > > Any ideas? Anybody got this issue before? It seems to be some (not obvious) > > permission problem. > > > > Below I type the whole procedure to install, so one can see that I followed > > all installation instructions. > > > > History: > > > > 1) Successfully downloaded and unzipped the files at /usr/loca/freesurfer > > > > 2) Successful set up of environment variables after including the following > > lines in .bashrc: > > > > ############################################## > > #Software FREESURFER - Enviroment variables > > # > > export FREESURFER_HOME=/usr/local/freesurfer > > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > export SUBJECTS_DIR=/home/theo/freesurfer/subjects > > ############################################## > > > > BTW, "theo" is my userID > > > > 3) File license.txt copied to /usr/local/freesurfer > > > > 4) message after open a terminal window confirms that Enviroment variables > > were correctly set: > > > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer > > FSFAST_HOME /usr/local/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > MNI_DIR /usr/local/freesurfer/mni > > (base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR > > /home/theo/freesurfer/subjects > > (base) theo@theo-Inspiron-5457:~$ > > > > > > Any help is welcome > > Regards > > > > Theotonio > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Theotonio Pauliquevis -
Tim Schäfer