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mrtools:surfacesandflatmaps [2013/07/28 14:11]
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 This section will give you an overview of how surfaces and flat maps work in MLR. You may wish to start by going through the [[:​mrTools:​TutorialsSurfacesAndFlatMaps|Surfaces and Flat Maps Tutorial]] before going through this page. This section will give you an overview of how surfaces and flat maps work in MLR. You may wish to start by going through the [[:​mrTools:​TutorialsSurfacesAndFlatMaps|Surfaces and Flat Maps Tutorial]] before going through this page.
  
-It is important to note that MLR is **not** a tool for segmenting 3D volumes and generating surfaces. You can use any tool that is capable of generating an outer (pial) surface and inner (boundary between gray and white matter) surface. If you have these two files, then you will be able to use the full functionality of surface and flat map visualization in MLR. We typically use FreeSurfer (see [[:​mrtools:​howto#​use_free_surfer_with_mlr|here]] for how to import) to generate segmentations. Jonas Larsson'​s [[http://​www.pc.rhul.ac.uk/​staff/​J.Larsson/​software.html|SurfRelax]] and Caret (see [[:​mrtools:​howto#​use_caraet_with_mlr|here]] to import) can also be used. Caret, however, only generates a mid-cortical surface and not both the inner and outer surfaces that are useful for displaying data at different cortical depths.+It is important to note that MLR is **not** a tool for segmenting 3D volumes and generating surfaces. You can use any tool that is capable of generating an outer (pial) surface and inner (boundary between gray and white matter) surface. If you have these two files, then you will be able to use the full functionality of surface and flat map visualization in MLR. We typically use [[http://​surfer.nmr.mgh.harvard.edu|FreeSurfer]] (see [[:​mrtools:​howto#​use_free_surfer_with_mlr|here]] for how to import) to generate segmentations. Jonas Larsson'​s [[http://​www.pc.rhul.ac.uk/​staff/​J.Larsson/​software.html|SurfRelax]] and Caret (see [[:​mrtools:​howto#​use_caraet_with_mlr|here]] to import) can also be used. Caret, however, only generates a mid-cortical surface and not both the inner and outer surfaces that are useful for displaying data at different cortical depths.
  
 3D surfaces and flat maps are used to display fMRI data from the gray matter of the cortex. They are a helpful visualization tool. But, it is important to understand that, surfaces and flat maps are **just** a visualization tool. MLR always keeps your data analyzed in the way it was collected -- in the coordinates of the original EPI images. Whenever you view data on a surface or a flat map, MLR is transforming your already analyzed data on the fly. 3D surfaces and flat maps are used to display fMRI data from the gray matter of the cortex. They are a helpful visualization tool. But, it is important to understand that, surfaces and flat maps are **just** a visualization tool. MLR always keeps your data analyzed in the way it was collected -- in the coordinates of the original EPI images. Whenever you view data on a surface or a flat map, MLR is transforming your already analyzed data on the fly.