Differences

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--- ajay:neuroelf_usage_notes [2014/03/24 15:18] – [Using the voxel rendering] ajay
+++ ajay:neuroelf_usage_notes [2025/01/21 02:00] (current) – [Exporting files to SPM, FSL, etc.] asatpute
@@ 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
@@ Line 490: / Line 497: @@
   - where the second argument, true, makes the output be written in TAL order, such that it complies with FSL's internal preference.
   - also works with vtc, glm, etc.
+==== Installing Neuroelf on Apple Silicon  ====
+. Update MAC OS
+. Update Matlab
+. Download neuroelf
+. You may run into issues with mexmaca64 files. You either have to tell OS that those files are allowed to be opened by trying to open them. Or you can delete all of them, install XCode, and then recompile the mexmaca64 files from scratch (see below).
+. in matlab, add path to the parent neuroelf directory (not with subdirectories)
+. then, save path
+. >>n = neuroelf
+. >>n.neuroelf_makelibs %this is to make the mexmaca64 files
+. >>neuroelf_setup