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|* figure out a better way to define RECON_CHECKER_SCRIPTS and scriptDirs....INSTEAD, set QA_SCRIPTS to be the QAtools directory, and then [[BR]] within the scripts set RECON_CHECKER_SCRIPTS to be $QA_SCRIPTS/data_checker/||
* figure out a better way to define RECON_CHECKER_SCRIPTS and scriptDirs....INSTEAD, set QA_SCRIPTS to be the QAtools directory, and then
within the scripts set RECON_CHECKER_SCRIPTS to be $QA_SCRIPTS/data_checker/ - DONE by jp 10/12/06
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....INSTEAD, set QA_SCRIPTS to be the QAtools directory, and then within the scripts set RECON_CHECKER_SCRIPTS to be $QA_SCRIPTS/data_checker/ - DONE by jp 10/12/06 * add greconversion and greconversions to ALWAYS run first when the recon-checker is run - DONE by jp on 09/29/06 * -outputfileorder appears to not work. - DONE by vp 10/10/06 * i think i can fix the snapshot script to make it run faster. - DONE by jp 10/12/06 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. * VP added 3 scripts to the data_checker directory: gnicv, gparcvalnorm, gparcmeannorm. Now the recon_all_aseg_outlier_checker now compares and looks for outliers after the segmentation volumes have been corrected for ICV, per David's suggestion
FreeSurfer QA Tools
QA mini-intro coming soon...
To check the output of one reconned subject
First you'll need to properly set your SUBJECTS_DIR. Also you'll need to set your QA_SCRIPTS directory. This should be the directory that you downloaded the QAtools directory. For our example here QAtools is in /space/tensor/17/users/jpacheco/QAtools.
setenv QA_SCRIPTS /space/tensor/17/users/jpacheco/QAtools
Now, from your SUBJECTS_DIR you are ready to run:
$QA_SCRIPTS/data_checker/recon_checker -nocheckasegoutliers -s bert -o QAsnap.html
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.
OutputsBR There will be two log files output into your subjects scripts directory:
ls bert/scripts recon_checker.bert.details.log recon_checker.bert.summary.log
The 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: /usr/local/freesurfer/dev/bin/recon-all In output_file_checker In recon_all_status_log_checker bert COMPLETE
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: /space/dijon/28/users/jpacheco/freesurfer_stable3_centos64//bin/recon-all In output_file_checker In recon_all_status_log_checker bert STEPS_MISSING
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.
The recon_checker.bert.details.log will give more details as to what might be wrong if there are problems. For the second subject above, with steps missing, the recon_checker.bert.details.log looks like:
------------------------------------------------------------- Running recon_checker on: Wed Oct 4 13:54:30 EDT 2006 Checking Last Version Used: /space/dijon/28/users/jpacheco/freesurfer_stable3_centos64//bin/recon-all Checking ALL Versions Used: /usr/local/freesurfer/dev/bin/recon-all, /space/dijon/28/users/jpacheco/freesurfer_stable3_centos64//bin/recon-all, In output_file_checker SUBJECTS_DIR is /autofs/space/tensor_014/users/jenni In recon_all_status_log_checker bert STEPS_MISSING 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 log shows that the dev version of FreeSurfer was used for a previous set of processing, but most recently the private version was used. The output from the
To check the output of a group of reconned subjects