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
 * i think i can fix the snapshot script to make it run faster.

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 mini-intro coming soon...

To check the output of one reconned subject

With your SUBJECTS_DIR set, run the following command from your SUBJECTS_DIR:

/space/tensor/17/users/jpacheco/QAtools/data_checker/recon_checker -nocheckasegoutliers -s bert -o QAsnap.html

where bert is your subject ID and QAsnap.html is the name of the output html file that you want to create.BR For complete usage instructions please see the ReconChecker page. BR

What it does: BR

OutputsBR There will be two log files output into your subjects scripts directory:

ls bert/scripts

recon_checker.bert.summary.log contains a summary of the status of that subject:

Running recon_checker on:
Thu Oct  5 15:00:42 EDT 2006
Checking Last Version Used:
In output_file_checker

In recon_all_status_log_checker

This subject was run most recently using the dev version of FreeSurfer and all the steps have been run. Another example of this log file is:

Running recon_checker on:
Wed Oct  4 13:54:30 EDT 2006
Checking Last Version Used:
In output_file_checker

In recon_all_status_log_checker

This subject was run most recently using a version of FreeSurfer located /space/dijon/28/users/jpacheco/freesurfer_stable3_centos64 and there are steps missing from the processing stream.


To check the output of a group of reconned subjects

To check the output of a group analysis

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 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.