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ajay:neuroelf_usage_notes [2014/02/04 00:26]
ajay [Using command lines to extract beta's from a glm and voi NeuroElf]
ajay:neuroelf_usage_notes [2016/08/03 22:36] (current)
ajay [Scripting and Batching: Tips and Pitfalls]
Line 374: Line 374:
   - to restrict stats to voxels with brain data, keep the multiplication box checked; potentially alter the minimum anatomical value to increase/​decrease visibility of stats around the border of the data   - to restrict stats to voxels with brain data, keep the multiplication box checked; potentially alter the minimum anatomical value to increase/​decrease visibility of stats around the border of the data
   - higher interpolation (cubic/​sinc) takes longer but gives also better quality output (mostly useful for higher resolution renderings);​ only set to sinc for final shot!   - higher interpolation (cubic/​sinc) takes longer but gives also better quality output (mostly useful for higher resolution renderings);​ only set to sinc for final shot!
 +
 +===== Using the new 3D rendering tool with skull =====
 +Jochen Email
 +  - download and install the latest snapshot: http://​neuroelf.net/​NE_14032023.zip
 +  - then use "​neuroelf_setup"​ and "​neuroelf_makefiles all" (without quotes)
 +  - when you next open the NeuroElf GUI, load the following VMR/​anatomical from the File -> Colin menu: colin_brain_rendskull_ICBMnorm.vmr and colin_hires_ICBMnorm.vmr
 +  - in the main UI, ensure that the colin_hires_ICBMnorm.vmr is selected
 +  - use the render button (below the surface view button) on the right side to switch to render view
 +  - in the newly open render UI, select the colin_brain_rendskull_ICBMnorm.vmr dataset as the "Alpha volume"​ (transparency information;​ dropdown close to the top)
 +  - once the rendering is complete, you can use the same controls as for the surface view (mouse; with shift to translate and alt to zoom; and also cursor keys)
 +
 +When you want to add a stats map (or several maps), please know that each map will be resampled into the resolution of the anatomical prior to rendering, so to display 3 stats maps (at the same time) on top of the high-res colin brain, you probably need between 2 and 3 GB free memory! Also, for stats maps, I suggest changing them to "​stats-dependent transparency"​ (pressing the "​n"​ key while in the slice-view, THEN selecting the map/s you want to show, and then switching to render view)
  
 ===== Drawing/​creating a mask ===== ===== Drawing/​creating a mask =====
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-==== 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;​   - clear the object between analyses. glm.ClearObject;​ mdm.ClearObject;​
   - '​bless'​ the command where you run the mdm: glm = bless(mdm.ComputeGLM(opts));​   - '​bless'​ the command where you run the mdm: glm = bless(mdm.ComputeGLM(opts));​
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   - INCORRECT: struct('​tfilter',​200,'​tfilttype','​dct','​motpars',​rps)   - INCORRECT: struct('​tfilter',​200,'​tfilttype','​dct','​motpars',​rps)
   - where rps is a cell array pointing to files name for realignment parameters   - 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
  
  
ajay/neuroelf_usage_notes.1391469984.txt.gz · Last modified: 2014/02/04 00:26 by ajay