# Code Backbone ``` lead.m ``` `lead.m` is the main function that calls the apps `lead_dbs.m`, `lead_connectome.m`, `lead_mapper.m`, `lead_group.m`. Thus, by calling `lead dbs`the function calls lead\_dbs.m ``` ea_run.m ``` …is the high-level "submit" function for any job submitted by lead DBS, lead connectome, lead mapper, lead anatomy etc (anything except `lead group` and `lead groupconnectome`). The function is also called when exporting code instead of actually running code and when using a "submit" function to submit code from the cluster. So basically, anything related to single-patient/subject analyses will pass through `ea_run`. ``` ea_autocoord.m ``` …is the main backbone of the pipeline that is then sometimes completed by `ea_write.m`. All functions that process data on a single level (i.e. do not stem from `lead group` or `lead groupconnectome`) branch off from `ea_autocoord`. As a side note, the name stems from the very early days in which lead dbs was still called "eAuto" for electrode autolocalization. The same is true for the prefix (`ea_*`) that we use in almost all functions. ``` ea_write.m ``` …is the final "writeout" function that exports 2D results or opens data in the 3D viewer `ea_elvis.m`. ``` ea_elvis.m ``` …is the 3D viewer of Lead-DBS. You can e.g. call it directly by running `ea_mnifigure.m`. ``` ea_handles2options.m ``` This is the function that converts handles (Matlab GUIDE handles to GUI elements) to the ubiquitous `options` struct that Lead-DBS uses to run jobs. For example the struct may contain `options.dicomimp.do == 1;` to let `ea_autocoord` know to run the DICOM import module. ## Other important main functions in Lead-DBS Most of the following branch off from `ea_autocoord` or `ea_elvis` – thus if you study these two a bit, you'll get a good feeling about the overall pipeline. ``` ea_dicom_import ``` …is the DICOM import module of the main GUI. ``` ea_imageclassifier ``` …opens the image classifier to rename Niftis that have been converted from DICOMs. ``` ea_lcm ``` …is the main subroutine to run everything related to `lead connectome mapper`. ``` ea_checkcoregallmri ``` …is the function to coregister preop MRIs of a specific patient. ``` ea_coregmr ``` …is the function used to coregister postop MRIs to preop MRIs of a specific patient. ``` ea_coregctmri_* ``` …all functions in this pattern will generate a CT to MRI coregistration entry in the main GUIs and will be called to perform the coregistration. They need to reside in the main lead-DBS code directory to be captured by the GUIs. If you want to create a new method to register CT to MRI, just duplicate one that is close and go from there. However, there are various things to consider, so maybe speak with us before/while you do. ``` ea_normalize_* ``` …similar with normalization methods: all files that match the above pattern found in the main code directory will create an entry for a normalization method in the GUIs. If you want to add such a method, duplicate on that is close and go from there. However, there are various things to consider, so maybe speak with us before/while you do. ``` ea_subcorticalrefine ``` …is the main function to run brainshift correction. ``` ea_checkcoreg ``` …is the function used when calling "Check Results" from the main GUIs. ``` ea_checkstructures ``` …is the function to open the "Refine atlas fit" function (which shows agreement between normalized patient images and specific atlas nuclei). This function can also be used to refine normalizations. ``` ea_runtraccore ``` …runs the main TRAC/CORE prereconstruction algorithm to detect leads. ``` ea_runpacer ``` …runs the PaCER prereconstruction algorithm to detect leads. ``` ea_runmanual ``` …runs the "Manual" preregistration module using SPM orthviews. ``` ea_runmanualslicer ``` …runs the "Manual" preregistration module using 3DSlicer. ``` ea_manualreconstruction ``` …main function of the manual reconstruction ("Localize DBS electrodes") view. ``` ea_orient_main ``` …main function of the DiODe rotation detection algorithm (Dembek et al) called from `ea_manualreconstruction`. ``` ea_writeplanes ``` Main 2D visualization output function ("Write out 2D") – while `ea_elvis` is the main 3D output function (see above). ## Preferences and Options ``` ea_prefs ``` Main function to get the prefs struct that is usually present as options.prefs. Prefs are defined by the function `.ea_prefs.m` in the user's home directory that is derived from `ea_prefs_default.m` in the lead-DBS code directory. You can open the user's prefs directory by hitting command/strg+P from a main GUI. If you need to add a prefs entry, make sure to add it to both `ea_prefs_default` and if needed to your own user prefs. `ea_prefs.m` will always combine entries from the two (if they are present in the user file, it will prefer these over the default prefs). ``` ea_prefs.mat ``` …along with the file `ea_prefs_default.mat` are analogous to the prefs text files (entry above) but more machine readable. That's why their content is stored in prefs.machine when calling `ea_prefs.m` (or in `options.prefs.machine` when in the main code somewhere). ``` options=ea_getptopts(directory,options) ``` …function to complete the `options` struct for patient-specific entries. For many things, you need only this limited `options` struct together with `options.prefs=ea_prefs;` ## Other functions that are often used and helpful to know ``` ea_assignpretra || [options,presentfiles]=ea_assignpretra(options); ``` …is a function to assign the preoperative images of a patient folder (e.g. used for normalization). ``` ea_save_reconstruction(coords_mm,trajectory,markers,elmodel,0,options); ``` …is the function to properly save electrode localizations ``` [coords_mm,trajectory,markers,elmodel,manually_corrected,coords_acpc]=ea_load_reconstruction(varargin) ``` …is the function to properly load electrode localizations ``` ea_view ``` …can be used to save and store a 3D camera view. ``` ea_chirp ``` …plays the "done" sound if the user has activated it in her/his prefs. ``` ea_busyaction ``` …function to show/hide a spinning wheel on the current GUI to show the user something is running. ``` ea_dispercent ``` …used to show progress of a for-loop in the console output.e ``` ea_dispt ``` …function that will display a text string in the console but also protocol time (when calling the function on multiple occasions throughout laborious work.