FreeSurfer QA Tools


QA Notepad

The QA Notepad program allows researchers to quickly take concise notes on subject or data derived from subjects in an organized, consistent manner. It is fully customizable and will work on an individual subject as well as a group of subjects.BR #The program is located in the folder ~dkoh, and is named QAnotepad. The source files are located in ~dkoh/QAstream. BR QA Notepad outputs text files with the extension .qa (unless you use the --noappend option).

QA Notepad options

  -h, --help: displays a help message
  -f, --file <filename>: name of output file (default: QAnotes)
  -s, --subj <subject1> <subject2> ... : enters a list of subjects to choose
                                         from when recording data.
  --subjfile <subject file>: specifies a file with a list of subjects.
  -u, --user <username>: name of user.
  -c, --config <config file>: input config file to customize interface
                              It is required to enter a custom output filename
                              if you use this option.
  --noappend: ".qa" will not be appended to the filename.
  --dbupdate: if this flag is set, QAnotepad will automatically update the
              memage database via ~dkoh/scripts/perl/

If you already have a list of the subjects you'll be editing, you can enter that list into QA Notepad through the -s or --subj option. Alternatively, you can create a file with a list of subjects, and pass the filename in through the option --subjfile.

Using Config Files


  Reoriented Yes No
  Realigned Yes No
  Manual_Edits None A_Few Lots
  Automatic_Segmentation Good Bad Corrected Good_For_Vol

This would create a panel with four buttons: Reoriented, Realigned, Manual_Edits, and Automatic_Segmentation. If you clicked on Automatic_Segmentation, you would get a new window with the options: Good, Bad, Corrected, Good_For_Vol. The underscores in place of spaces are mandatory, as the program separates options with spaces and won't be able to tell the difference. BR attachment:QAnotepad_example.jpg BR

If you want to have a free text field as an option for what to save, enter "$freetext" as an option after one of the option headers, like so:

  Region_Edited Hippocampus Amygdala $freetext

If you want to have a custom title for your window, just put the following text on it's own line:

$title My Title Here

attachment:QA_notepad2.jpg BR

This will output a simple text file, that is tab delimited and contains all the information that you entered for each subject.

Subject      User          Reoriented    Realigned    Manual_Edits    Automatic_Segmentation
bert         jpacheco      Yes           Yes          A_Few           Good_For_Vol              your own text here!!
subject2     jpacheco      No            Yes          None            Good_For_Vol              Hippocampus

Automatic Database Updates

If you use the flag --dbupdate with the standard configuration of QA Notepad, it will automatically update the memage database to match your file. It will only update the subjects in your file that already exist in the database. It does so via the perl script, located at ~dkoh/scripts/perl/

Updating Custom Configurations

If you want to have your custom configuration updated in the database, first, create a procedure with User Defined Select data that matches your custom configuration. Then, determine your procedure's id number. You can do this from one of two places. From the page where you edit the steps of your procedure, if you look at the url, there should be a part after the ? which says pprocedure=NUMBER. That number is your procedure's id. You can also find this from the page on which you edit the subject. Once you have your procedure id, put this on its own line in your config file:

Where ID is the procedure id that you found earlier. If you don't do this step, you will get an error message.

Recon Checker

The recon checker will run for one subject, or a group of subjects, and performs a relatively thorough QA check on the outputs of a FreeSurfer cortical reconstruction. It will verify the FreeSurfer version used on each subject and check for the existance and order of all the files that should have been created in the recon process. It will identify any outliers from subcortical segmentation volumes. It will then take snapshots of your recon and store them in a specified output file, allowing you to see an html report of all the subjects you have run.

Recon Checker Options

    -sf <subject file>: specify a file with a list of subjects. May be used
                        instead of -s or -subjid to specify subjects.
    -outputfileorderfile <file order file>: specify a file which lists the
                        proper order of the output files.
    -ignore <process1 to ignore> <process2 to ignore> ...: specify processes
                        to ignore
    -detailed: take a more detailed set of snapshots
    -overwrite: take all snapshots, even if there are previously taken ones.
    -genoutputorderfile: generate the file order from the first subject.
    -snapshotsonly: control program execution