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| #acl JenniPacheco:read,write,delete,revert BradDickerson:read,write,delete,revert DavidSalat:read,write,delete,revert VasanthPappu:read,write,delete,revert | = FreeSurfer 5.3 QA Tools = |
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| == STATUS == | == Deprecated == Note: The QA tools described in this page were developed for !FreeSurfer 5.3. For versions 7+, use the following executable to compute QA stats: |
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| 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. |
qatools.py --help |
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| = FreeSurfer QA Tools = [[TableOfContents]] QA mini-intro coming soon... |
<<TableOfContents>> |
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| == 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. ----- '''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 ''**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.'' ----- |
The QA Tools are intended to be used in assessing the quality of one or more FreeSurfer recons. These scripts are capable of verifying all steps in the FreeSurfer recon-all stream were executed and in the correct order, as well as verifying all files exist and were created in the correct order. Additionally, these scripts can be used to detect potential outlier regions in the aseg.mgz within a dataset, calculate SNR and WM intensity values, and collect detailed snapshots of various volumes. The following people have been major contributors in developing these scripts: David Koh, Stephanie Lee, Jenni Pacheco, Vasanth Pappu, and Louis Vinke. |
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| The QA Tools scripts are a work-in-progress. Any feedback, bug reports, or feature requests are appreciated (email vinke[at]nmr.mgh.harvard.edu). | |
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| == To check the output of a group of reconned subjects == | Click [[QuickQaQdec|here]] to view steps for an alternate QA procedure using Qdec. |
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== To check the output ofa 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]] #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/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: |
== Setup == Click the link below to download the QA Tools scripts. Extract all the contents of the tar file into a new directory. Source your local version of FreeSurfer, set your subjects directory variable, and set the QA Tools path: |
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| Region_Edited Hippocampus Amygdala $freetext }}} |
<source freesurfer> |
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| 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 }}} |
In tcsh: setenv SUBJECTS_DIR /path/to/your/subjects_dir setenv QA_TOOLS /path/to/QATools/scripts |
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| 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. == 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. -checkstatuslog -nocheckstatuslog -checkoutputfiles -nocheckoutputfiles -takesnapshots -notakesnapshots -snapshotsonly: control program execution |
In bash: export SUBJECTS_DIR=/path/to/your/subjects_dir export QA_TOOLS=/path/to/QATools/scripts |
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| ==== Check FreeSurfer Versions ==== | [[attachment:QAtools_v1.2.tar.gz]] === Dependencies === QA Tools requires: * !ImageMagick Studio version 6.2.8 or higher when using the snapshots option. This can be downloaded [[http://www.imagemagick.org/script/index.php|here]]. * The GNU awk (gawk) utility. This can be downloaded [[http://www.gnu.org/software/gawk/|here]]. == Getting Started == Run the following command to view explanations for all the QA Tools options: {{{ $QA_TOOLS/recon_checker -help }}} By default QA-Tools will check the status log, the order files were created, the aseg for any outliers, create snapshots of slices throughout various volumes, and calculate SNR and WM measures. See the flags below if you want to disable one or more of these options. == Arguments == === Required Flagged Arguments === ||-s <subject1> [<subject2>...] ||Case ID for one or more subjects located in $SUBJECTS_DIR (use -s-file as alternative) || |
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| ==== Check Status Log ==== This will go through your subjects {{{scripts/recon-all-status.log}}} and verify that you've run the steps in the correct order. If you have it will display a message like this: {{{ In recon_all_status_log_checker subject1 COMPLETE }}} If there is a problem with the order of steps in the {{{recon-all-status.log}}} it will display a message like this: {{{ In recon_all_status_log_checker subject2 STEPS_MISSING }}} It will also output where the mishap is and perhaps offer some further information about what was run: {{{ Expected to see the following steps before #@# Tessellate rh Wed Jun 7 14:43:02 EDT 2006 in the recon-all-status.log file (line # 98): --> Tessellate lh --> Smooth1 lh --> Inflation1 lh --> QSphere lh --> Fix Topology lh --> Make Final Surf lh --> Smooth2 lh --> Inflation2 lh --> Cortical ribbon mask lh --> Sphere lh --> Surf Reg lh --> Contra Surf Reg lh --> AvgCurv lh --> Cortical Parc lh --> Parcellation Stats lh --> Cortical Parc 2 lh --> Parcellation Stats 2 lh However, these LH processes were executed previously. Perhaps the RH output was modified and re-run without re-running the LH processes. }}} This is a quick way to check whether everything was run in an appropriate order or not. ==== Check Output Files ==== fails because no aseg look up option ==== Identify Aseg Outliers ==== where is the aseg mean look up table. can we add a flag for these options. ==== Take Snapshots ==== |
=== Optional Flagged Arguments === ||-subjid <subject1> [<subject2>...] ||Specify subject(s) to process || ||-s-file ||Specify a file with a list of subjects. May be used instead of -s or -subjid || ||-snaps-out ||Full path and name of snapshots HTML file. Default: "$SUBJECTS_DIR/QA/QA_check.html" || ||-snaps-detailed ||Take a more detailed set of snapshots || ||-snaps-overwrite ||Take all snapshots, overwriting any existing snapshots || ||-no-snaps ||Do not take snapshots || ||-snaps-only ||Only take snapshots || ||-outputFOF <file-order list> ||Specify a file which lists the proper order of output files || ||-asegLUT <file> ||Specify a file containing aseg outlier lookup table || ||-gen-outputFOF ||Generate the file order list from the first subject || ||-gen-asegLUT <file> ||Generate an aseg look up table from your subjects that can be used to identify aseg outliers || ||-nocheck-aseg ||Do not check for aseg outliers || ||-nocheck-status ||Do not check status log file for each subject || ||-nocheck-outputFOF ||Do not check output order of files for each subject || ||-nocheck-SNR-WM ||Do not calculate SNR and WM measures for each subject || ||-completeStatusFile <file> ||Compares each subject's status log file to the specified log file || ||-completeStatusFiles <file> ||Compares each subject's status log file to each of the complete status logs listed in <file> || ||-ignore <process1> [<process2> ...] ||Specify one or more FreeSurfer processes to ignore while checking status files || |
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| ==== Output Files ==== | == Future Directions == * Implement -gen-status flag * Shorter alternative flags * Handle cases where FS ran multiple times (status_file_checker) * Generate status log file from specified subject * Create file order and status step lists for longitudinal QA * Snapshots taken using Freeview * Specify snapshots be taken of specific regions found in aparc+aseg.mgz with Freeview * Automatically adjust intensity/contrast of volumes before taking snapshots * Compile snapshots into GIF animations * Detect outliers in aparc and aparc2009 volumes * Handle cases where two files flip/flop in creation order (output_file_checker) * WM/SNR measurement outputs to seperate file (tab-delimited) * Make image & html links for snapshots relative so directory can be moved or renamed == Release Notes == v1.1 (3/5/2012) * Log and screen output modified * Created default file order list for *.long subject folders processed with FSv5.1 (default_FOF_FSv5.1_long) == Known Issues == * To get the "-gen-asegLUT" flag of 'recon_checker' to work on FS 5.3 data, you need to change the helper 'gnicv' script to grep on "!EstimatedTotalIntraCranialVol" rather than "ICV" (due to the name change of that variable in the stats/aseg.stats file relative to FS 5.1). * When taking snapshots, the tkmedit and tksurfer windows that appear can't be blocked by other windows, and the screensaver can't be activated while these scripts are running. Otherwise, the script will take snapshots of the screensaver or the interfering windows. The monitor can be physically turned off while the scripts are running, however, to save power. == For internal users == If you want to disable your screensaver so snaps can be taken overnight, set the value in . ~/.gconf/desktop/gnome/session/%gconf.xml to the number of minutes you want to pass before your screensaver activates (eg 960 for 16 hours). Also, go to System Preferences -> Screensaver and click on Power Management. In the "On AC Power" tab, choose Never in both of the pull down menus. |
FreeSurfer 5.3 QA Tools
Deprecated
Note: The QA tools described in this page were developed for FreeSurfer 5.3. For versions 7+, use the following executable to compute QA stats:
qatools.py --help
Contents
The QA Tools are intended to be used in assessing the quality of one or more FreeSurfer recons. These scripts are capable of verifying all steps in the FreeSurfer recon-all stream were executed and in the correct order, as well as verifying all files exist and were created in the correct order. Additionally, these scripts can be used to detect potential outlier regions in the aseg.mgz within a dataset, calculate SNR and WM intensity values, and collect detailed snapshots of various volumes. The following people have been major contributors in developing these scripts: David Koh, Stephanie Lee, Jenni Pacheco, Vasanth Pappu, and Louis Vinke.
The QA Tools scripts are a work-in-progress. Any feedback, bug reports, or feature requests are appreciated (email vinke[at]nmr.mgh.harvard.edu).
Click here to view steps for an alternate QA procedure using Qdec.
Setup
Click the link below to download the QA Tools scripts. Extract all the contents of the tar file into a new directory. Source your local version of FreeSurfer, set your subjects directory variable, and set the QA Tools path:
<source freesurfer> In tcsh: setenv SUBJECTS_DIR /path/to/your/subjects_dir setenv QA_TOOLS /path/to/QATools/scripts In bash: export SUBJECTS_DIR=/path/to/your/subjects_dir export QA_TOOLS=/path/to/QATools/scripts
Dependencies
QA Tools requires:
ImageMagick Studio version 6.2.8 or higher when using the snapshots option. This can be downloaded here.
The GNU awk (gawk) utility. This can be downloaded here.
Getting Started
Run the following command to view explanations for all the QA Tools options:
$QA_TOOLS/recon_checker -help
By default QA-Tools will check the status log, the order files were created, the aseg for any outliers, create snapshots of slices throughout various volumes, and calculate SNR and WM measures. See the flags below if you want to disable one or more of these options.
Arguments
Required Flagged Arguments
-s <subject1> [<subject2>...] |
Case ID for one or more subjects located in $SUBJECTS_DIR (use -s-file as alternative) |
Optional Flagged Arguments
-subjid <subject1> [<subject2>...] |
Specify subject(s) to process |
-s-file |
Specify a file with a list of subjects. May be used instead of -s or -subjid |
-snaps-out |
Full path and name of snapshots HTML file. Default: "$SUBJECTS_DIR/QA/QA_check.html" |
-snaps-detailed |
Take a more detailed set of snapshots |
-snaps-overwrite |
Take all snapshots, overwriting any existing snapshots |
-no-snaps |
Do not take snapshots |
-snaps-only |
Only take snapshots |
-outputFOF <file-order list> |
Specify a file which lists the proper order of output files |
-asegLUT <file> |
Specify a file containing aseg outlier lookup table |
-gen-outputFOF |
Generate the file order list from the first subject |
-gen-asegLUT <file> |
Generate an aseg look up table from your subjects that can be used to identify aseg outliers |
-nocheck-aseg |
Do not check for aseg outliers |
-nocheck-status |
Do not check status log file for each subject |
-nocheck-outputFOF |
Do not check output order of files for each subject |
-nocheck-SNR-WM |
Do not calculate SNR and WM measures for each subject |
-completeStatusFile <file> |
Compares each subject's status log file to the specified log file |
-completeStatusFiles <file> |
Compares each subject's status log file to each of the complete status logs listed in <file> |
-ignore <process1> [<process2> ...] |
Specify one or more FreeSurfer processes to ignore while checking status files |
Future Directions
- Implement -gen-status flag
- Shorter alternative flags
- Handle cases where FS ran multiple times (status_file_checker)
- Generate status log file from specified subject
- Create file order and status step lists for longitudinal QA
- Snapshots taken using Freeview
- Specify snapshots be taken of specific regions found in aparc+aseg.mgz with Freeview
- Automatically adjust intensity/contrast of volumes before taking snapshots
- Compile snapshots into GIF animations
- Detect outliers in aparc and aparc2009 volumes
- Handle cases where two files flip/flop in creation order (output_file_checker)
- WM/SNR measurement outputs to seperate file (tab-delimited)
Make image & html links for snapshots relative so directory can be moved or renamed
Release Notes
v1.1 (3/5/2012)
- Log and screen output modified
- Created default file order list for *.long subject folders processed with FSv5.1 (default_FOF_FSv5.1_long)
Known Issues
To get the "-gen-asegLUT" flag of 'recon_checker' to work on FS 5.3 data, you need to change the helper 'gnicv' script to grep on "EstimatedTotalIntraCranialVol" rather than "ICV" (due to the name change of that variable in the stats/aseg.stats file relative to FS 5.1).
- When taking snapshots, the tkmedit and tksurfer windows that appear can't be blocked by other windows, and the screensaver can't be activated while these scripts are running. Otherwise, the script will take snapshots of the screensaver or the interfering windows. The monitor can be physically turned off while the scripts are running, however, to save power.
For internal users
If you want to disable your screensaver so snaps can be taken overnight, set the value in
- ~/.gconf/desktop/gnome/session/%gconf.xml
to the number of minutes you want to pass before your screensaver activates (eg 960 for 16 hours). Also, go to System Preferences -> Screensaver and click on Power Management. In the "On AC Power" tab, choose Never in both of the pull down menus.