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Dear Lorenzo, I'm glad to hear that the solution worked and thank you for correcting the path. Best regards, Kiyotaka 2019/02/21 23:56 Lorenzo <[log in to unmask]>: > Thank you Kiyotaka, it worked! > > However, in case it could be useful to someone, at least in my case, I had > to write > > . /etc/fsl/5.0/fsl.sh > > as it was the correct path in my computer. > > Thank you again for the help and for the explanation. > > Best, > > Lorenzo Mancuso > Il 21/02/2019 15:23, Kiyotaka Nemoto ha scritto: > > Dear Lorenzo, > > 1) Quick answer: > > Since you use Lubuntu 18.04, open terminal and type > > leafpad ~/.bashrc > > > to open a text editor. > > Then add the following line to .bashrc > > . /etc/fsl/fsl.sh > > (Don't forget the period at the beginning of the line) > > Save and close the file, then reboot your PC. > > Then you will be able to use fslutils. > > > 2) Background for the answer: > > For Debian and Ubuntu families, two different versions of FSL are > available. One is from FSL team, and the other is from Neurodebian. > Neurodebian FSL is available up to 5.0.9, which you install on your system. > > In order to use fslutils on neurodebian FSL, you need to add '. > /etc/fsl/fsl.sh' to your ~/.bashrc . > > As of installation of original FSL (from FSL team), you need to use > fslinsataller.py which you can get after registration on FSL website. > fslinstaller.py requires python2, which is not shipped with Ubuntu 18.04 > (it comes with python 3), so you need to install python2 first. > > sudo apt install python (This is described in > https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux) > > However, as your error message says, it seems fslinstaller.py does not > support 32-bit version of Ubuntu any more (though I may be wrong), > so solution for your system is to use FSL from Neurodebian. > > Hope this helps, > > Kiyotaka > > > 2019/2/21 22:53 Lorenzo Mancuso <[log in to unmask]>: > >> Dear Tim, >> >> yes, I'm using the default Ubuntu shell. It seems to me that there is >> some installation issue, as the output of echo $FSL_DIR (and also of echo >> $FSLDIR, as suggested in the wiki page) returns an empty line. This is the >> output for echo $PATH: >> >> >> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin >> >> A thing that I forgot to mention is that FSL is named on my computer as >> fsl-5.0-core, which seems a bit odd to me. I tried to reinstall using the >> python script, but I did not found on the internet a script for FSL 5.0, >> and the script for FSL 6.0 gives an error (ubuntu i686 not supported). I >> reinstalled through apt-get, and I noticed a series of errors related to >> the grub that I did not spot last time I installed it. The output is >> partially in Italian but I hope that the global sense of it is >> understandable: >> >> errore: memoria esaurita. >> errore: syntax error. >> errore: Incorrect command. >> errore: syntax error. >> Errore di sintassi alla riga 303 >> Errori di sintassi sono stati rilevati nel file di configurazione >> di GRUB generato. Assicurarsi che non vi siano errori in >> /etc/default/grub e /etc/grub.d/* o segnalare un bug allegando >> il file /boot/grub/grub.cfg.new. >> dpkg: errore nell'elaborare il pacchetto grub-pc (--configure): >> installed grub-pc package post-installation script subprocess returned >> error exit status 1 >> Elaborazione dei trigger per man-db (2.8.3-2ubuntu0.1)... >> Configurazione di fsl-5.0-core (5.0.9-5~nd18.04+1)... >> Si sono verificati degli errori nell'elaborazione: >> grub-pc >> E: Sub-process /usr/bin/dpkg returned an error code (1) >> >> It says that it detects syntax errors in the GRUB configuration file, and >> that there is an error in the elaboration of the package grub-pc. >> >> I also added to the .profile file the lines reported in FAQ wiki >> (FSLDIR=/usr/local/fsl ecc.), however it did not help as there is no fsl >> directory in /usr/local. I found two directories named fsl, one in /usr/lib >> containing only the directory 5.0, and another in /usr/share containing the >> directories 5.0 and data. I don't know if one of these two is my >> installation folder (the one in share looks more convincing). I tried to >> change the content of .profile writing share or lib instead of local but >> nothing changed: echo $FSLDIR always returns an empty line and fslmaths is >> always a command not found. >> >> >> There is some solution to all this? Thank you in advance for any answer >> >> Sincerely >> >> Lorenzo Mancuso >> >> >> Il 18/02/2019 22:14, Tim Schäfer ha scritto: >> > Dear Lorenzo, >> > >> > it could be that all that's missing is that your shell is not setup >> correctly, i.e., the FSL environment variables may not be set correctly and >> the FSL bin directory may not be part of your PATH. >> > >> > 1) Which shell are you using? I assume bash, the Ubuntu default shell? >> > >> > 2) Could you report the output of the following 2 commands: >> > - echo $FSL_DIR >> > - echo $PATH >> > >> > I do not know about the neurodebian package, but if you installed from >> the python script and did not change the default location, your FSL >> installation should be in /usr/local/fsl/. In that case, you should be able >> to run flsmaths by typing: >> > >> > /usr/local/fsl/bin/fslmaths >> > >> > (But you should definitely get the shell setup fixed.) >> > >> > Best, >> > >> > Tim >> >> ######################################################################## >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> >> > > -- > Kiyotaka Nemoto, M.D., Ph.D. > Associate Professor > Department of Psychiatry > Division of Clinical Medicine, Faculty of Medicine > University of Tsukuba > 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan > E-mail: [log in to unmask] > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> Mail > priva di virus. www.avg.com > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > <#m_-2571725236167356957_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: [log in to unmask] ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1