FMRI navigation

Preprocessing

• These notes apply to 140.115.47.153

Creating alias

• Create alias of commands (or “shortcuts”), under the home directory, use the nano command to edit a configuration file:

nano .tschrc.aclexp

• Add to the bottom of the file:

alias <name_of_shortcut> <‘your command’>

• Replace contents within <> to suit your need. For example:

alias cdnav ‘cd /media/DATA1/navigation’

allows you to type just “cdnav” (without the quotes) to change directory from anywhere to /media/DATA1/navigation. You will have to reinitiate another instance of terminal for the new settings to be effective.

GUI interface

• You can initiate a graphic user’s interface (gui) of file manager by typing:

nautilus

• Or a gui editor by typing

gedit

• Note that when you initiate a gui in a terminal, you won’t be able to type new commands in that terminal. You can initiate another terminal from the SSH client gui.

Reconstructing rawdata into AFNI format

• Change working directory to the navigation folder

cdnav

• Change working directory to the script folder

cd scripts

• edit the participants list

nano subjlist.txt

• To 3D

python to3d_anat.py <numid>

-numid: numerical code of the participant.

python to3d_func.py <numid>

-numid: numerical code of the participant.

Creating stimulus time files

• Change working directory to the scripts folder

cd /media/DATA1/navigation/scripts

-Or just type “cd scripts”, if you have followed settings in previous slides to change directory to /media/DATA1/navigation

• Creat stimulus time files

python mkcond1D03.py <numid> <group id> 

-numid: numerical code of the participant (001, 002, … etc)

-group id: group code of the participant (allo or ego )