I am working on juptyter notebook in my VSCODE and when I try to run a command line in a cell as the following:
!'directory of fsl software' -I 'path of the mask in the MNI space' -o 'path of output file -w 'path of transformation from MNI to subjects mask' -r 'path of subject mask' --interp=nn
However, when I run the code, I obtain the error:
ERROR:: Environment variable FSLOUTPUTTYPE is not set! Please make sure that the appropriate configuration file is sourced by your shell (e.g. by putting it in .profile). e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh" e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh"
As it indicates, I open on VSC the file .bash_profile in the editor and copy:
FSLDIR=/usr/local/fsl . ${FSLDIR}/etc/fslconf/fsl.sh PATH=${FSLDIR}/bin:${PATH} export FSLDIR PATH
and, after saving the .bash_profile file and re running the line, it still doesn't work. Any idea?
I downloaded the Conda package of fslpy but I didn't use it because I'm running a command line and also I checked the dimensions of the files I was working with and that's not either the problem. I tried to download the VSCode extension in the remote server I am working with of FSharo fsl and fsy but obtained no results
Related
I want to copy a folder ~/Projects/LocalProject onto my server //VM-Server/ServerProject.
I know that I can use GitBash:
cp -r directory-name-1 directory-name-2
But what I'm curious about is, can I create a script to do that by double clicking that script, or adding it as a command to my GitBash, cause I will need that alot?
--Edit--
Tried nothing, as I don't know how to do that. Yes there are hidden files, I don't want them to be copied. There shouldn't be newer files on the destination. I need to manually run it, I thought that's clear as I mentioned the option to have a executable script / or a terminal command.
Option 1: Batch file
You don't even need git-bash; you can make a batch file in any text editor, name it copy to server.bat, and type in cp C:\Users\<Your username>\Projects\LocalProject \\VM-Server\ServerProject.
You can also make a .sh file for use in bash. The command is the same, just make note that Windows uses \, while bash uses / for directory tree
Option 2: Alias
Open your bash_profile file (it's in your git bash install location).
Add a line at the end of the file that says alias copyToServer = 'cp ~/Projects/LocalProject //VM-Server/ServerProject'. Then close git-bash, reopen it and use the command by typing copyToServer as a bash command. (It doesn't need to be named copyToServer)
I'm currently using this terminal command to open Matlab:
open -a MATLAB_R2020a (whenever I'm not in the Applications directory)
Does there exist a way to shorten the command? i.e. open Matlab by using the following terminal command:
open matlab
or
open -a matlab
Also, I'm not sure if this is relevant, but I'm using Mac OS Catalina 10.15.4.
You can start MATLAB by running its startup shell script:
/Applications/MATLAB_R2020a.app/bin/matlab
If you want to shorten this, add the /Applications/MATLAB_R2020a.app/bin/ directory to your PATH environment variable, then you can start MATLAB by just typing matlab:
export PATH=$PATH:/Applications/MATLAB_R2020a.app/bin/
matlab
The line that starts with export PATH can be added to your ~/.profile file.
There may be other ways, but here is one that I know of which is called bash scripting
simply open a new file (lets call it 'thefile.sh' and write the following lines inside;
#!/bin/bash
open -a MATLAB_R2020a
Then run the following command to make it executable
chmod +x thefile.sh
now you can simply run
./thefile
and it will just do that. You will be able to call this command from the directory where it is located, but if you wish to make it accessible from anywhere, just by using terminal, move it to the following location:
/usr/local/bin
I hope this answers your question.
I was downloading the CakePHP framework for a project. Below the steps:
Installation
1) Install PHP 5.6 from: http://php-osx.liip.ch/
curl -s http://php-osx.liip.ch/install.sh | bash -s 5.6
2) add the updated PHP version to our path. So we edit .profile file
nano ~/.profile
Add into the file
export PATH= /usr/local/php5/bin:$PATH
Then hit Control + O to write out the file
Then hit Control + X to save the file
exit
Restart the Terminal
Now the terminal doesn't work as usually. I've tried to understand the shell concept and apply different solutions, but I can't even find the .profile file again.
I obtain errors like:
enter code here-bash: ls: command not found
Anybody can explain me what's wrong and the shell concept to properly understand shell (-bash)?
The problem is this:
export PATH= /usr/local/php5/bin:$PATH
You killed your PATH variable. You need to find a way to edit .profile file, and change that line to:
export PATH=$PATH:/usr/local/php5/bin
You could try editing with the following command (using vim):
/usr/bin/vim /Users/yourname/.profile
Or (using nano):
/usr/bin/nano /Users/yourname/.profile
Or just remove .profile file completely by doing /bin/rm /Users/yourname/.profile. Of course, in any case, you need to restart your terminal once you're done.
I try to work with a project in vagrant.
I have made the command vagrant ssh, and connected to VM. Now I need to edit .bashrc file to set path to the source code. But first I couldn't find that file. So I googled and find that the way is call command ~/.bashrc. But doing this I get message, that I have no access to it:
[vagrant#nupic-vagrant:~]$ ~/.bashrc
-bash: /home/vagrant/.bashrc: Permission denied
So what to do now?
UPD.
I can't find the .bashrc file.
When I try to make command ls -a I get following:
[vagrant#nupic-vagrant:~]$ ls -a
. .bash_logout cleanup.sh sshd.sh .veewee_params
.. .bash_profile minimize.sh vagrant.sh .veewee_version
.bash_history .bashrc .ssh .vbox_version .zsh_profile
[vagrant#nupic-vagrant:~]$ locate .bashrc
/etc/skel/.bashrc
/home/vagrant/.bashrc
/var/chef/backup/etc/skel/.bashrc.chef-20130614181911
/var/chef/backup/home/vagrant/.bashrc.chef-20130614181912
[vagrant#nupic-vagrant:~]$
But only the place where I can find some of those files is the directory where cygwin is installed. Pls, see illustrations, they reflect relations between directories vagrant and cygwin.
.bashrc is not meant to be executed but sourced. Try this instead:
. ~/.bashrc
or, equivalently
source ~/.bashrc
See the reference about the . (aka source) builtin.
Note that if what you're looking for is to restart your Bash session after modifying your ~/.bashrc file, you might as well use:
exec bash
That will replace your current Bash session (thanks to exec) by a new session.
If you want to edit that file (or any file in generally), you can't edit it simply writing its name in terminal. You must to use a command to a text editor to do this. For example:
nano ~/.bashrc
or
gedit ~/.bashrc
And in general, for any type of file:
xdg-open ~/.bashrc
Writing only ~/.bashrc in terminal, this will try to execute that file, but .bashrc file is not meant to be an executable file. If you want to execute the code inside of it, you can source it like follow:
source ~/.bashrc
or simple:
. ~/.bashrc
If you can't access the file and your os is any linux distro or mac os x then either of these commands should work:
sudo nano .bashrc
chmod 777 .bashrc
it is worthless
The .bashrc file is in your user home directory (~/.bashrc or ~vagrant/.bashrc both resolve to the same path), inside the VM's filesystem. This file is invisible on the host machine, so you can't use any Windows editors to edit it directly.
You have two simple choices:
Learn how to use a console-based text editor. My favourite is vi (or vim), which takes 15 minutes to learn the basics and is much quicker for simple edits than anything else.
vi .bashrc
Copy .bashrc out to /vagrant (which is a shared directory) and edit it using your Windows editors. Make sure not to save it back with any extensions.
cp .bashrc /vagrant
... edit using your host machine ...
cp /vagrant/.bashrc .
I'd recommend getting to know the command-line based editors. Once you're working inside the VM, it's best to stay there as otherwise you might just get confused.
You (the vagrant user) are the owner of your home .bashrc so you do have permissions to edit it.
Once edited, you can execute it by typing
source .bashrc
I prefer to logout and in again (there may be more than one file executed on login).
Please find the step to fix bash restricted error on Linux servers.
If you are getting below restricted message while try to login to the server by using your credentials , then it might be an issue with lack of directory permissions in the server.
Because of this permission issue we were unable to navigate to required directories and getting error “bash: cd: restricted”
Fix : To release bash restriction error use the highlighted command in Linux server -bash -f
As same if wants to restrict the permission use the highlighted command - bash -r
Once you executed the bash -f command the restrictions will be released from the directories and we can able to proceed with patch scripts.
Is it possible to run Matlab commands from Mac command line?
The matlab script is in the bin subdirectory of the MATLAB app bundle. On my machine, this means I can run it like so:
/Applications/MATLAB_R2012a_Student.app/bin/matlab
If you want this bin directory on your path (so that you can just run matlab, mex, etc), edit or create a new text file called .bash_profile in the top level of your home directory with the following line:
export PATH=/Applications/MATLAB_R2012a_Student.app/bin:$PATH
Replacing the "MATLAB_R2012a_Student" part with the name of your actual MATLAB app bundle. This will not come into effect for currently open terminals, but newly opened terminals should work properly.
You need the full path to the MATLAB executable, and you can use the -r option to run a command in the MATLAB that you start, as per the doc here.
As already mentioned above you need to first edit your .bash_profile file by adding the following line (replace 'MATLAB_R2020b' with your MATLAB version)
export PATH=/Applications/MATLAB_R2020b.app/bin:$PATH
Then after restarting the terminal you can open MATLAB by inserting the command
/Applications/MATLAB_R2020b.app/bin/matlab
You can also run your .m scripts by defining the working directory folder and the executable scripts and their paths. You just need to add more commands to the above.
/Applications/MATLAB_R2020b.app/bin/matlab -r "addpath(genpath('{Your working directory folder path}')); cd {Your working directory folder path}; {Your script name}; {Your other script name}; quit;"
Please find a more detailed description of MATLAB command line arguments from:
https://www.mathworks.com/help/matlab/ref/matlabmacos.html#d122e801165