Adding a New fMRI Pre-Processing Protocol

(1) Find a pre-existing protocol that is most similar to the new one you'd like to create, and make a copy of it. Give the copy a descriptive name. The rest of these instructions will be applied to the copy; leave the original unchanged. For example, if you'd like to make a new version of the IR1_ProtocolFile.txt protocol with 20 mm smoothing rather than the usual 8 mm, you might run the following commands:

 

 

(2) Open up the new protocol file in your favorite text editor, e.g. gedit, vi, emacs, etc. E.g.,

 

 

(3) Edit the new protocol file to conform to your desired changes. E.g., if you want to point it to a new processing pipeline such as /export/w/apps/tcl/FixedEffectsPipeline_v3_NoMC.tcl, change the line

 

 

to

 

 

(4) By default, the ResultsDirectory is set to DefaultAnalysis. This is the subdirectory in the Results directory in which HS2 pre-processed data will be written. You might want to change this to some other directory name, e.g. AnalysisWithNoMC or JeremysNewAnalysis, especially if you have already pre-processed this data and it has already generated stuff in a DefaultAnalysis subdirectory.

 

(5) Save the changes and exit the editor.

 

(6) Load the file /export/w/apps/tcl/PresetsList.txt into your text editor. Add a new line at the bottom pointing to the new protocol file. For example, if you just created and edited a new protocol file named IR1_20mm_Smoothing_ProtocolFile.txt in the directory /export/w/apps/tcl, you'd add the following line to the bottom of the PresetsList.txt file:

 

 

(7) Save the changes and exit the editor.

 

(8) Now when you run HS2, the new protocol will show up at the bottom of the Presets list. To use it, simply select it as usual.