scripts are all here:

*they should all be working now.

 *add a flag for -noasegoutlier - DONE by vp on 9/28/06
 *make version checker scripts output to the same log file as recon_checker - DONE by jp on 9/29/06
 *figure out a better way to define RECON_CHECKER_SCRIPTS and scriptDirs
 *add greconversion and greconversions to ALWAYS run first when the recon-checker is run - DONE by jp on 09/29/06

Things I've done:
 *I've created the pages ReconChecker and QAnotepad which will be the only place that full usage options for these scripts will be, eventually

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

Check FreeSurfer Versions

Check Status Log

This will go through your subjects scripts/recon-all-status.log and verify that you've run the steps in the correct order. If you have it will display a message like this:

In recon_all_status_log_checker
subject1 COMPLETE

If there is a problem with the order of steps in the recon-all-status.log it will display a message like this:

In recon_all_status_log_checker

It will also output where the mishap is and perhaps offer some further information about what was run:

Expected to see the following steps before
#@# Tessellate rh Wed Jun 7 14:43:02 EDT 2006
in the recon-all-status.log file (line # 98):
--> Tessellate lh
--> Smooth1 lh
--> Inflation1 lh
--> QSphere lh
--> Fix Topology lh
--> Make Final Surf lh
--> Smooth2 lh
--> Inflation2 lh
--> Cortical ribbon mask lh
--> Sphere lh
--> Surf Reg lh
--> Contra Surf Reg lh
--> AvgCurv lh
--> Cortical Parc lh
--> Parcellation Stats lh
--> Cortical Parc 2 lh
--> Parcellation Stats 2 lh
However, these LH processes were executed previously.
Perhaps the RH output was modified and re-run without re-running the LH processes.

This is a quick way to check whether everything was run in an appropriate order or not.

Check Output Files

fails because no aseg look up option

Identify Aseg Outliers

where is the aseg mean look up table. can we add a flag for these options.

Take Snapshots

Output Files