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Overlaying FSL Feat statistical maps

In this exercise, the data set of subject bert is used for demonstration. To begin the exercises, first enter the following directory, and then set the current directory to be the default subjects directory using this command:

cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
setenv SUBJECTS_DIR ${PWD}

1.0 Overlaying the statistical map onto the bert's orig volume

Use the following command to display the zmap (zstat1.img) overlaid onto the bert's orig volume. It will display the automatic segmentation, and will also set the threshold at z = 2.3:

 tkmedit bert orig.mgz lh.white -aux brain.mgz \
   -overlay ./fbert.feat/stats/zstat1.nii.gz \
   -overlay-reg ./fbert.feat/reg/freesurfer/anat2exf.register.dat \
   -segmentation ${SUBJECTS_DIR}/bert/mri/aparc+aseg.mgz ${FREESURFER_HOME}/FreeSurferColorLUT.txt \
   -fthresh 2.3 -fmid 3.3 -fslope 1 

You should see the image below:BR attachment:tkm-zstat1-cor-128.th23.small.jpg When you click or mouse over a voxel, the cortical or subcortical structure that that voxel belongs to will be displayed in the control panel. You can view any of the volumes in the stats dir in this way as well as the clustered maps in the feat directory.

2.0 View statistical maps on bert's surface

To view any of the statistical maps on bert's surface, run:

tksurfer bert lh inflated \
  -overlay ./fbert.feat/stats/zstat1.nii.gz \
  -overlay-reg ./fbert.feat/reg/freesurfer/anat2exf.register.dat \
  -fthresh 2.3 -fmid 3.3 -fslope 1

You should see the image below:BR attachment:tks-zstat1-rh-lat.th23.small.jpg To load the cortical parcellation, goto File->Label->Import Annotation, and enter lh.aparc.annot. The parcellation will be opaque. To show only the ouline (as above), View->LabelStyle->Outline.When you click or mouse over a vertex, the control panel will display the name of the cortical structure. You can view any of the volumes in the stats dir in this way as well as the clustered maps in the feat directory. You can also run the tkmedit and tksurfer commands above in separate shells and use the SavePoint/GoToPoint functionality to navigate through the volume and surface.

In order to display the statistical map overlaid onto the surface, the data in fbert.feat must be resampled. This is done with feat2surf. Documentation for what it does and how it does it can be obtained with:

feat2surf --help

To run it on this data set, run:

feat2surf --feat fbert.feat --target fsaverage

Verify that this has created four directories under fbert.feat: reg_surf-lh, reg_surf-rh, reg_surf-lh-fsaverage, and reg_surf-rh-fsaverage. Each one of these directories will have a stats directory in which all the statistics from fbert.feat/stats have been resampled onto the surface. The fsaverage directories are resampled onto the common surface spaced (defined by fsaverage).

3.0 Viewing statistical maps on bert's surface

To view the statistical maps on the right hemisphere, run tksurfer:

tksurfer bert rh inflated \
  -o ./fbert.feat/reg_surf-rh/stats/zstat1.mgh  \
  -fthresh 1.3 -fmid 2.3 -fslope 1

Note that you can run the above tkmedit command (from a different window) simultaneously with the tksurfer command to visualize the same data on the volume and in the surface. You can then use the Save/Goto Point buttons to navigate between the surface and volume.

You should see the image below:BR attachment:tks-zstat1-rh-lat-small.jpg

4.0 Overlaying zmap onto the FSL's standard volume

You can also use tkmedit to view your results on the FSL standard volume instead of the individual's anatomical with the following command:

tkmedit -f $FSLDIR/etc/standard/avg152T1_brain.img \
     -overlay ./fbert.feat/stats/zstat1.nii.gz \
     -overlay-reg ./fbert.feat/reg/freesurfer/std2exf.register.dat \
     -fthresh 1.3 -fmid 2.3 -fslope 1