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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 = 1.3:

tkmedit bert orig -aux brain -overlay ./fbert.feat/stats/zstat1.img \
    -overlay-reg ./fbert.feat/reg/freesurfer/anat2exf.register.dat \
    -fthresh 1.3 -fmid 2.3 -fslope 1 \
    -segmentation ${SUBJECTS_DIR}/bert/mri/aseg ${FREESURFER_HOME}/FreeSurferColorLUT.txt

You should see the image below:BR attachment:tkm-zstat1-cor-128-small.jpg

2.0 Sampling statistical maps onto bert's 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

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 -overlay-reg-identity \
  -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.img \
     -overlay-reg ./fbert.feat/reg/freesurfer/std2exf.register.dat \
     -fthresh 1.3 -fmid 2.3 -fslope 1