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draw_surface_roi.md

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Draw ROIs on surface in FreeSurfer 7.1.0 or later (via freeview)

FreeSurfer needs to be set up properly at first (steps).

Then following steps should be repeated for each subject, analysis, contrast, and threshold. For example, we will draw a label of face-vs-object contrast (f-vs-o) for subj1 on the left hemisphere (lh) with the threshold of 2 (i.e., 0.01).

  1. Run the FreeSurfer command: tksurfer-sess -s subjfunc -a analysis.lh -c f-vs-o -fthresh 2.

    • tksurfer-sess: the command to open the data file of a particular session;
    • -s (or -subject): subject name in the functional data;
    • -a (or -analysis): analysis name in the subject name folder;
    • -c (or -contrast): name of the contrast within the analysis folders;
    • -fthresh: the threshold used to show the overlay (2 is corresponding to p<0.01).
    • Then a freeview window will open and display an inflated brain with the overlay.

  2. Based on the reference coordinates for the specific ROI, left click the activation cluster that is/includes the ROI.

    • You may rotate the brain by clicking and move your mouse (before clicking the cluster).

  3. [IMPORTANT!!!] Please make sure Annotation is turned off.

    • You may turned it off by select Off in the dropdown list.

  4. Click the Custom Fill icon, which is at the left upper corner, just below the brain surface or volume files.

    • A new window called Custom Fill will open; select Up to functional values below threshold and then click Fill.

  5. Then you should see a new label named label_1 showed up in the Label section.

    • You may change the label name by clicking the label name, e.g., label_1.

  6. Save this label.

    • More options -> Save As...
    • Select where you would like to save the label and rename the label. Click Save.

  7. Done. Just close the freeview window.


Draw ROIs on surface in FreeSurfer 6.0 or earlier (via tksurfer)

FreeSurfer needs to be set up properly at first (steps).

Then following steps should be repeated for each subject, analysis, contrast, and threshold. For example, we will draw a label of face-vs-object contrast (f-vs-o) for subj1 on the left hemisphere (lh) with the threshold of 2 (i.e., 0.01).

  1. Run the FreeSurfer command: tksurfer-sess -s subjfunc -a analysis.lh -c f-vs-o -fthresh 2 -tksurfer.
    • tksurfer-sess: the command to open the data file of a particular session;
    • -s (or -subject): subject name in the functional data;
    • -a (or -analysis): analysis name in the subject name folder;
    • -c (or -contrast): name of the contrast within the analysis folders;
    • -fthresh: the threshold used to show the overlay (2 is corresponding to p<0.01).
    • -tksurfer: only include this option when using FreeSurfer 6.0 (but not for earlier versions).
    • Then a tksurfer window will open and display an inflated brain with the overlay.

  2. Based on the reference coordinates for the specific ROI, left click the activation cluster that is/includes the ROI.
    • You may rotate the brain by clicking the curly arrows (before clicking the cluster).

  3. Click the Custom Fill icon, which is at the middle of the second row.
    • A new window called Custom Fill will open; select Up to functional values below threshold and then click Fill.

  4. Save this label.
    • File -> Label -> Save Selected Label...;
    • Select where you would like to save the label and rename the label. Click OK.

  5. Done. Click File -> Quit to quit.

Draw ROIs on surface with custom functions

Please refer to help file for fs_drawlabel().