Differences

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--- ajay:neuroelf_usage_notes [2014/02/03 23:26] – [Using command lines to extract beta's from a glm and voi NeuroElf] ajay
+++ ajay:neuroelf_usage_notes [2014/03/24 15:18] – [Using the voxel rendering] ajay
@@ 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
   - 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 =====