= Working notes on Albert, Ivry, Miall?, Brett paper =

Codename '''rechoicey'''

== State of the data ==

=== Locations ===

 * avalon.bham.ac.uk (behind a firewall) at `/home/avalon/albertn/data/rechoicey`
 * Neil's external disk at home, accessible, from Linux, as `mount -t cifs //192.168.1.117/Neil/Experiments/FMRI/Choicey /mnt/neil -o user=name,password=pass`

We'll call this file location CHOICEYROOT

== Behavioral data ==
 * Within `CHIOCEYROOT/behavior` there is a summary sheet called `Choicey_behavior.xls`. This file is the file exported after merging the individual eprime data (edat) files.
 * Default E-Prime output files are located in `CHOICEYROOT/behavior/edat/<subjectid>`:
   * Individual edat files exist for each run for each subject. 
   * Individual run-time e-prime log files (text files). '''missing .txt''': subjects 35-37.
 * User created outupt files are located in `CHOCEYROOT/<subjectid>/refs`: 
   * the event timing log files (.dat) that is ouput from e-prime. 
   * the .ref file which has converted the above into info to `groovy_batch` models.
   * the .rtm file (reaction time matched reference file) for `groovy_batch` models.

 * Within the directory, directory above, eprime files in `CHOICEYROOT/data/behavior`
 * edat files for all runs, txt files (with identical information) for all but subjects 35-37. Edat and equivalent txt files record full log of events in eprime.  
 * There were also .dat files written out from the script, with information selected by the script. These are in `CHOICEYROOT/data/refs/<subjectid>` 
 * Matlab processed versions of these files became the .ref files for the analysis - `CHOICEYROOT/<subjectid>/refs`

 * ''NOTES:''  Subject 29OM needs to have recovery of the behavioral data and also will need to get the PostFix.OnsetDelay and timing mode for PostFix and its logging of "mouse" responses.

Some data, and code to analyze the files above in http://imaging.mrc-cbu.cam.ac.uk/svn/choiceyana/devel


== Subjects ==

 1. 21AW
 1. 22JS
 1. 23JX
 1. 24EC
 1. 25AM
 1. 26ZD
 1. 27FR
 1. 28MH
 1. 29om (EXCLUDE '''?''': didn't finish experiment - 4 sessions)
 1. 30AP
 1. 31FP (EXCLUDE '''?''': didn't vary self selection)
 1. 32AW
 1. 33LA
 1. 34TJ
 1. 35NL
 1. 36HW (EXCLUDE '''?''': Image artifact? earings?)
 1. 37MH
 
== Literature review ==

All studies using PET or FMRI to study internal / external selection.  Studies looking at internal / external timing excluded, unless they independently look at selection.   For each paper:

 * Thumbnail description of task.  Concentrating on nature of baseline, any potential difficulty confounds, whether preparation matched.  Note differences in task RTs
 * For each subtraction, note activation coordinates and Z / t scores in medial premotor cortex (SMA, preSMA, anterior cingulate (Z > 0, abs(X) < 10, Y > -20?), premotor cortex (dorsal or ventral).  
 * Note modality, template, coordinate frame / normalization (MNI, Talairach, etc)
 * Results (as reported, including negatively) of Internal - Rest, External - Rest, Internal - External , External - Internal.  Note lack of report as well as 'no significant activation'.  Note threshold used for each. 

See DefiningSma