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== Scripts == == FreeSurfer Scripts ==

FreeSurfer Scripts

tkmedit tcl script

As mentioned in the course, you can create a tcl script to use with tkmedit or tksurfer so that they open with your preferences already selected (such as surface color, surface thickness, etc.). Below is an example of a tcl script that interacts with tkmedit:

SetZoomLevel 2

SetSurfaceLineColor 0 0 0 0 1
SetSurfaceLineColor 1 0 0 0 1
SetSurfaceLineWidth 0 0 2
SetSurfaceLineWidth 1 0 2
SetSurfaceLineWidth 0 2 2
SetSurfaceLineWidth 1 2 2
SetDisplayFlag 5 0
SetCursorColor .5 0 .5

The above script does the following things (the order below corresponds to the order of each line in the script above):

  • Zooms in once
  • RedrawScreen applies this zoom

  • Sets one hemisphere of the white surface to blue
  • Sets the other hemisphere of the white surface to blue
  • Sets one hemisphere of the white surface to a thickness of 2
  • Sets the other hemisphere of the white surface to a thickness of 2
  • Sets one hemisphere of the pial surface to a thickness of 2
  • Sets the other hemisphere of the pial surface to a thickness of 2
  • Turns off the original surface
  • Changes the cursor (+) to purple

The script can be created in any text editor (i.e. emacs, vi, gedit) and should be saved with the tcl extension (i.e. surfaces.tcl) in a convenient location.

A list of other options that can be added to the script are here: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting

In order to use the script, you would call it using the -tcl flag with your tkmedit command. For example:

 tkmedit subj001 brainmask.mgz -aux T1.mgz -surfs -tcl /path/to/surfaces.tcl


If you find yourself typing the same commands over and over, a nice shortcut is to make an alias for it. An alias is a short nickname for the full command. For example, instead of typing out the command ls -l each time you want to use it, you can create an alias for it like this:

alias l "ls -l"

Now, if you type l and hit enter in a terminal, you'll get the same response as you would if you typed ls -l.

For every new terminal window you open, you will have to type the above command again in order for it to work. To avoid this, you can create a text file with all the aliases you commonly use. This file will need to be saved in your home directory with the name:


You're not done yet. You also need to source that text file within your configuration file (i.e. .cshrc or .bashrc found in the home directory). You would add this line to that file:

source ~/.alias

Now, every time you open a new terminal window, it will automatically source your alias file.

Below are some ideas for aliases you may find useful:

alias  ../..  'cd ../..'
alias  ../../..  'cd ../../..'
alias  e  emacs
alias  ..  cd ..
alias  unpack  'unpacksdcmdir -src . -targ . -scanonly scan.log'
alias fvwm "freeview -v brainmask.mgz wm.mgz:colormap=heatscale -f ../surf/lh.white:edgecolor='blue' ../surf/rh.white:edgecolor='blue' ../surf/lh.pial:edgecolor='red' ../surf/rh.pial:edgecolor='red'"

(Note: That last alias is intended to be all on one line.)

For the below, \!* indicates to substitute it with whatever is typed on the commandline.

alias fv 'freeview \!*'

So if you typed:

fv  orig.mgz

The alias will work as if you typed freeview orig.mgz. Similarly, you could use:

alias tkm "tkmedit \!* brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.white -segmentation aseg.mgz -segmentation-opacity 0.2 -tcl ~/surfaces.tcl"

And only have to type tkm subj001 to open a subject with tkmedit.

This alias will set the SUBJECTS_DIR variable to whichever directory you are currently in.

alias  sd 'setenv SUBJECTS_DIR `pwd`'

The below alias illustrates that one alias could do multiple things. In this case, you can source FreeSurfer, change directories to where your subjects are located and set the SUBJECTS_DIR variable all by simply typing fs.

alias fs 'setenv FREESURFER_HOME /home/apps/freesurfer; source $FREESURFER_HOME/SetUpFreeSurfer.csh; cd /home/apps/freesurfer/subjects; setenv SUBJECTS_DIR /home/apps/freesurfer/subjects'

Finally, the aliases below may be useful but they will only work if they always remain at the bottom of your alias file:

alias subdir 'echo $SUBJECTS_DIR'
alias fshome 'echo $FREESURFER_HOME'
alias csubdir 'cd $SUBJECTS_DIR'
alias cfshome 'cd $FREESURFER_HOME'

Batch Processing with recon-all

The script below is an example of how you can search for a subject's MPRAGE among several dicoms and then automatically create the recon-all command with its name and location. This script works with the way dicoms at the Martinos Center used to be named. It assumes the dicoms have been unpacked and searches the unpack log file for the typical MPRAGE dimensions, 256 x 256 x 128. From that location, it can find the name of the MPRAGE dicom (the 8th field in the log file, hence awk '{print  $8}') and prints it to a log file with the specified recon-all command.

set s = $1
setenv SUBJECTS_DIR /path/to/your/data
set log = $SUBJECTS_DIR/recon-all-commands.log
set dcmdir = /path/to/your/dicoms
set subjid = `echo $s |gawk -F- '{print $2}'`

if (-e $dcmdir/$s/scan.log) then
    echo "found scan.log, finding mprages"
    set dat = $dcmdir/$s/scan.log
    echo "no scan.log"

set mpr = (`cat $dat | grep "256 256 128" |grep ok | awk '{print  $8}'`)
echo "found mprages, $mpr"

echo recon-all -i $dcmdir/$s/$mpr -all -s $subjid >> $log

FsTutorial/Scripts (last edited 2016-11-04 17:13:29 by AllisonMoreau)