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 )

Running Preprocessing & Single-subject GLM

• To carry out all preprocessing steps

-cutting out TR (pb00), outlier screening, normalization (pb01), realignment (pb02), spatial smoothing (pb03), and scaling (pb04)

./proc.prep <groupid> <initials+date> 

-groupid: the participant’s group (allo/ego)

-initials+date: participant’s initials followed by date (e.g. LPS141109 ).

• To carry out single-subject (first level) GLM

./proc.glm <groupid> <numid> <initials+date> 

-groupid: the participant’s group (allo/ego)

-numid: numerical code of the participant

-initials+date: participant’s initials followed by date (e.g. LPS141109 ).

Checking & saving results

• Change to group.allo folder

cdreva

-you need to create this alias

• Change to group.ego folder

cdreve

-you need to create this alias

• Change to folder of the participants you would like to see and save the results

./@ss_review_basic > review_<id> .txt

-id: name+date – LPS141109 -save results

./@ss_review_driver 

-check brain images

Details of checking files

• Average outlier frac :

-notice if > 0.05

• Average motion :

-notice if > 1

• Fraction censored per run :

-notice if > 0.1

Details of checking images

• Check whether there are spikes or ghosts from the brain image.

• Check ghosts with “pb00” files from afni

• Check spikes : change to folder of the participants

./@epi_review.<ID> 

-ID: initials+date – LPS141109

-after checking a run, press enter on command window to go through the next run and so on.

Saving to Excel

• Save these three information to the excel worksheet ()

-Number TRs above not limit

-Number TRs above out limit

-Censor fraction