STATUS

scripts are all here:
/autofs/space/tensor_017/users/jpacheco/QAtools 

 * they should all be working now.

To-Do:
 * 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

TableOfContents

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

• checks the version of FreeSurfer used to process this subject

• checks the recon-all-status.log file to be sure each step was run

• checks the order of the output files to be sure that they were created in the correct order
• takes snapshots of the talairach, skullstrip, surfaces, curvature, and parcellations
• outputs two different log files and an html file (called QAsnap.html in this example) with the snapshots

  • **NOTE: while it takes the snapshots tkmedit and tksurfer will flash up on the screen. You do not need to do anything, the snap shots are taken automatically. To ensure good quality snapshots make sure there are no other windows over the tkmedit/tksurfer windows.

Outputs

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/load_QA.pl.

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

• You can customize the options in QA Notepad by using config files. The config file should be formatted with the option header in the first column, followed by the desired options. The option header will not appear unless it has at least one option. Here's an example config file. To pass in the config file, use the -c or --config option. If you use a config file, you must also specify an output file name with the -f or --file option.

example.cfg:

  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 load_QA.pl, located at ~dkoh/scripts/perl/load_QA.pl.

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:

• $procedure_id ID

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