ajay:neuroelf_usage_notes
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ajay:neuroelf_usage_notes [2013/10/21 12:49] – [Using the surface rendering] ajay | ajay:neuroelf_usage_notes [2016/08/03 20:27] – [Scripting and Batching: Tips and Pitfalls] ajay | ||
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- Then...< | - Then...< | ||
- | voi_betas = glm.VOIBetas(voi);</ | + | voi_betas = glm.VOIBetas(voi); |
- | + | %or to get all the beta maps not limited to a voi | |
+ | betas = glm.GLMData.Subject(S).BetaMaps(:,:,:,: | ||
+ | </ | ||
==== Using command lines to extract design information from glm NeuroElf ==== | ==== Using command lines to extract design information from glm NeuroElf ==== | ||
- glm.SubjectPredictors provides names of predictors | - glm.SubjectPredictors provides names of predictors | ||
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- plot(mdm.Handles.SDMs{1}.SDMMatrix) :this plots the matrix. | - plot(mdm.Handles.SDMs{1}.SDMMatrix) :this plots the matrix. | ||
- corrcoef(mdm.Handles.SDMs{1}.SDMMatrix(:, | - corrcoef(mdm.Handles.SDMs{1}.SDMMatrix(:, | ||
- | ===== Visualization | + | ===== Visualization |
+ | |||
+ | ==== Scripting Output Displays ==== | ||
+ | For outputting many slices for several maps, this section describes how to script the output visuals at the command line. | ||
+ | |||
===== Using the surface rendering ===== | ===== Using the surface rendering ===== | ||
- load up your VMP and threshold it (height threshold) | - load up your VMP and threshold it (height threshold) | ||
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- to restrict stats to voxels with brain data, keep the multiplication box checked; potentially alter the minimum anatomical value to increase/ | - to restrict stats to voxels with brain data, keep the multiplication box checked; potentially alter the minimum anatomical value to increase/ | ||
- higher interpolation (cubic/ | - higher interpolation (cubic/ | ||
+ | |||
+ | ===== Using the new 3D rendering tool with skull ===== | ||
+ | Jochen Email | ||
+ | - download and install the latest snapshot: http:// | ||
+ | - then use " | ||
+ | - when you next open the NeuroElf GUI, load the following 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" | ||
+ | - 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 " | ||
===== Drawing/ | ===== Drawing/ | ||
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- | ==== Scripting and Batching: | + | ==== Scripting and Batching: |
- | Sometimes we may want to run multiple glms changing one or another option. | + | |
+ | Verify the parameters for you GLM. In the command line, once you load the glm (E.g. by using >>glm = xff(' | ||
+ | - glm.Study(1).RunTimeVars.Predictors' | ||
+ | - glm.RunTimeVars | ||
- | If this is what you want to do, BE SURE TO DO THESE TWO THINGS | + | 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; | - clear the object between analyses. glm.ClearObject; | ||
- ' | - ' | ||
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- INCORRECT: struct(' | - INCORRECT: struct(' | ||
- 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. | ||
ajay/neuroelf_usage_notes.txt · Last modified: 2016/08/03 20:36 by ajay