Initiate phys_gui by using the command phys_gui_working
A figure will pop up which looks something like this: Select your monkey from the dropdown menu
Select the session folders you want to process after hitting the “Add date from list” button
If you hit “Run”, phys_gui will do all the preprocessing that you checked (see below) on the selected folders

In later TDT software versions (synapse - setup 3), the folder naming is different. For converting folders recorded with synapse to the old (our standard) folder naming, check the box “RenameSynapseTankNameToOldTankFormat”.

If you want to use the waveclus pipeline, you first need to create waveclus sortcodes. You can do so by checking “WCFromBB”. Folders (WC_Block-N) will be created for each block N, and one additional folder (WC) will contain the clustered data, concatining for each channel separately all blocks where the electrode was in certain range

If you want (or have) to use the online detected snippets, check “PLXFromSnippets”. If you first want to Realign your snippets to the minima, check “PLXFromRealignedSnippets” instead. PLX Files will be called Date_blocks_N.plx or Date_Realigned_blocks_N respectively.

After you sorted with waveclus, you can create a plexon file from your saved sortcodes. Check “PLXFromWCFromBB”. PLX Files will be called Date_from_BB_blocks_N.

After you are done with sorting, you can synchronize your recorded data with behavioral data, adding LFP and spike information in the trial structure format that monkeypsych uses. Check “CombineTDTandMP”.
In order to indicate which type of sorting you want to use, select one option in the “Choose spikes” section
“Snippets” uses the sortcodes based on the original snippets
“Realigned” uses the sortcodes based on realigned snippets
“FromBB” uses the sortcodes based on WC clustered PLX files
Choose “none” in case you are only interested in LFP. No spikes will be added to your combined data.

There is also an option for disregarding LFP. If you select this option, LFP data in the combined file will not be updated (in case it has been processed previously) or completely left out (if it hasn't been processed before). Use this option as long as you are resorting. You can also add LFP dat at a later point.

Check “CreateExcelEntries” for creating/updating the automatic sorting sheet of the respective Excel sorting table with the selected data (sessions). Only works after you did all the preceding steps.