Rendering functional data on surfaces (with Caret)

The following is an excerpt from the Caret tutorial located here (22Sept version; pages 67 and following).

This is a step-by step guide to taking a result you obtained in (say) FSL and rendering it on the Caret surface. Of course you should have downloaded the SEPTEMBER06 Caret tutorial data on your computer.

I’ve made a couple tweaks reflecting the fact that my data is typically in FSL format, orientation etc.

Also, here is another very helpful tutorial on the same topic

Part 5: Specific/selected analysis procedures

Caret has numerous options for analyzing data in ways that create new files or modify existing ones. Part

5 illustrates how to carry out a few commonly used major operations. Additional options are covered in

The Caret 5.5 User Guide to Analysis Procedures.

5.1 Mapping fMRI volume data – Average Fiducial and Multi-Fiducial Mapping.

  • Select Attributes: Map Volume(s) to Surface(s)
  • In the Map Volumes to Surfaces window press Next (accepting the default selection of ‘Metric (Functional) Data’).
  • In the Volumes Selection: Volume Thresholding section, check the box next to Enable Entry of Volume Threshold.
  • In the Volumes Selection: window press Add Volumes from Disk.
  • Select the following two fMRI volumes (in fact, select whatever is your stat-file from FSL!): BURTON_04_VibroTactile_EARLY_BLIND+orig.HEAD and BURTON_04_VibroTactile_SIGHTED+orig.HEAD and press Open.
  • Enter 3.5 for the positive threshold and -3.5 for the negative threshold for each of the selected volumes (or whatever else is appropriate for your data, you can always change this later). Note: The choice of threshold is up to the investigator, and typically should represent a cutoff for statistically significant voxels.
  • Press Next.
  • Press Map to Spec File with Atlas.

This will map data to your atlas of choice, and enter the resultant metric file(s) into the chosen spec file.

  • In the Atlas Surface Selection window, select Output Spec File: Human.PALS_B12.BOTH.Test-MapfMRI.73730.spec file. Select Open.
  • Select Mapping Atlas: space: FLIRT, then select Mapping Atlas: Atlas: PALS_B12 Multi-Fid Map LEFT hemisphere.
  • Press OK

Note on target spaces. The available atlas spaces include 711-2B [Colin], 711-2C, SPM2, SPM99, SPM96, SPM95 FLIRT, MRITOTAL, and AFNI versions of stereotaxic space. If, for example, your data are in the afni version of Talairach space (i.e., with ‘+tlrc’ in the file name), then choose Mapping Atlas: AFNI space. If your data are in the Washington University 711-2B space, use Mapping Atlas: 711-2C space (711-2B and 711-2C are essentially equivalent in this context.). For comments on the differences among these spaces, see The mapper also can be used to map data from an individual subject from the volume to the surface.

  • Press Map to Spec File with Atlas again, then select the same output spec file as before (…BOTH.Test-Map-fMRI…)
  • Select Mapping: Atlas: Space: FLIRT and Mapping Atlas: PALS_B12 Multi-Fid RIGHT hemisphere

This will result in both hemispheres being processed concurrently.

  • Then press Next in the Spec File and Surface Section page
  • In the Mutli-Fiducial Mapping Metric Output, leave the default selections: ‘Show Mapping to Average Fiducial Surface’ and ‘Show Average of Mapping to All Multi-Fiducial Cases’ options selected. The other output options are largely self-explanatory and are generally needed only in special circumstances.
  • In the Data File Naming: Data File text box, highlight and delete the default name (map_data_0…..metric) then enter a more informative name (you’ll have to look for this file, so give it a name that makes sense!): map_data_Grp_Contrast1_left_flirt.metric, then press SAVE.
  • Highlight the newly entered metric file and copy just the filename (not the directory)
  • Press the Surface Family pulldown menu and select the second entry (ending in “right FLIRT”)
  • Highlight and delete the default file name (map . . .), then paste in the previously copied metric file name (map_data_Grp_Contrast1_left_flirt.metric)
  • Change ‘LEFT’ to ‘RIGHT’ in the new metric file name.
  • Double-click on the first entry under Data Column Comment (AverageFiducial . . . ) to see a text editor showing the default contents of the comment for that column. Importantly, whatever comment exists in the volume file to be mapped is automatically included, along with additional information about the surface mapping. This comment can be edited if desired.
  • Press OK, (or Cancel) to close the text editors
  • Press Next at the bottom of the Data File Naming Window
  • Press the Mapping Algorithm: Enclosing Voxel pulldown menu, and note that there are many options available. [The various mapping algorithms available on the Mapping Algorithm page are explained more fully at – MappingAlgorithms]
  • Select Mapping Algorithm: Metric Enclosing Voxel, (the default option)
  • Review the Summary, press Finish.

5.1.3 Viewing fMRI mapping results

  • Select the Display Control: Scene page, then select the fourth scene (FLAT PALS-B12-BOTH…). This will set various parameters to a useful starting state for the next stage of visualization, but without initially showing any metric data.
  • Select File: Open Data File: Metric, select the Results directory, then press Open map_data_Grp_Contrast1_left_flirt.metric and press OK.
  • Similarly, openmap_data_Grp_Contrast1_right_flirt.metric (file in the RESULTS subdirectory) and press OK
  • Select the D/C button in the Main Window’s Toolbar.
  • Select the Display Control: Overlay/Underlay – Surface page.
  • Select Metric as the Primary Overlay.
  • Select the Display Control: Metric page.
  • Select the Apply Metric L-to-L, R-to-R Matching
  • Press the Metric: Selection tab
  • Select the first column (AFMLEFT.. .). The highlighted button will jump to the corresponding AFM RIGHT-column. This is OK because L-to-L, R-to-R matching is selected.
  • Select the second column (MFM-LEFT) –BURTON_04_VibroTactile_EARLY_BLIND to see the difference between AFM and MFM mapping of these data