Differences

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--- ajay:neuroelf_usage_notes [2014/03/24 15:18] – [Using the voxel rendering] ajay
+++ ajay:neuroelf_usage_notes [2016/08/03 20:36] (current) – [Scripting and Batching: Tips and Pitfalls] ajay
@@ Line 469: / Line 469: @@
-==== Scripting and Batching: Dangers  ====
+==== Scripting and Batching: Tips and Pitfalls ====
-Sometimes we may want to run multiple glms changing one or another option.
-If this is what you want to do, BE SURE TO DO THESE TWO THINGS
+Verify the parameters for you GLM. In the command line, once you load the glm (E.g. by using >>glm = xff('*.glm')), you can ensure the parameters (e.g. motion correction as covariates, percent signal change transform, filter type and implementation, etc.) using the following two locations in the glm object.
+  - glm.Study(1).RunTimeVars.Predictors'
+  - glm.RunTimeVars
+Sometimes we may want to run multiple glms changing one or another option. If so, BE SURE TO DO THESE TWO THINGS:
   - clear the object between analyses. glm.ClearObject; mdm.ClearObject;
   - 'bless' the command where you run the mdm: glm = bless(mdm.ComputeGLM(opts));
@@ Line 480: / Line 483: @@
   - INCORRECT: struct('tfilter',200,'tfilttype','dct','motpars',rps)
   - where rps is a cell array pointing to files name for realignment parameters
+  - VERIFY YOUR GLM using the methods indicated above.
+If your scripting is running inordinately slow, it may be because NeuroElf is loading, closing, and re-loading relevant data for a given step in your code. For example, when obtaining the betas from a glm for a set of vois, if you iterate across the vois to load the GLM, then it may reload all the GLM data each time. This is because NeuroElf runs efficiently by not loading up all the data unless it really needs to, but if you're coding, then you need to specify that. Use the following:
+   >>glm.LoadTransIOData