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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).
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  mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh \
    --iv fbert.feat/stats/cope1.nii.gz fbert.feat/reg/freesurfer/anat2exf.register.dat
mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh \
  --iv fbert.feat/stats/cope1.nii.gz fbert.feat/reg/freesurfer/anat2exf.register.dat
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This will create lh.cope1.nii.gz. In this case it will have only one frame, but if you had multiple runs or subjects, then you would add more --iv arguments pointing to the other volumes.
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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
}}}

[wiki:FsTutorial top] | [wiki:FsTutorial/FslFeatFreeSurfer previous]

  • To follow this exercise exactly be sure you've downloaded the [wiki:FsTutorial/Data tutorial data set] before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.

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 BR 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 Save-Point/Goto-Point functionality to navigate through the volume and surface.

3.0 Resampling COPEs to common surface

When performing surface-based group analysis of functional data, the COPEs must be sampled to the common surface space (similar to how you must reslice the COPEs from the native functional space into standard space prior to group analysis). The surface sampling can be done in two ways.

First, you can use feat2surf as in:

feat2surf --feat fbert.feat --cope-only

This will create fbert.feat/reg_surf-lh-fsaverage/stats for the left hemi (and another for the right). There will be cope1.nii.gz. This looks like a volume because it is in nifti format, but it is really a surface stored in a volume format (note it's dimensions are 1974 x 1 x 83 = 163842 = number of vertices in fsaverage's surface). You can then concatenate these files from different subjects to perform group analysis with FreeSurfer's mri_glmfit or FSL's randomise or flame.

Alternatively, when you have multiple runs/subjects, you can use mris_preproc, something like:

mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh \
  --iv fbert.feat/stats/cope1.nii.gz fbert.feat/reg/freesurfer/anat2exf.register.dat

This will create lh.cope1.nii.gz. In this case it will have only one frame, but if you had multiple runs or subjects, then you would add more --iv arguments pointing to the other volumes.

FsTutorial/OverlayFeatStatisticalMaps (last edited 2021-09-22 11:40:04 by DevaniCordero)