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I wish to thank everyone who took the time to respond to my request. It seems that thee are a number of different ways and packages to disguise a person's face.
Among the community the Adobe Premier products seem to be popular. Among the free software Virtualdub and VideoMach are recommended. Although I hadn't thought about it myself, those with a bit of knowledge of Matlab have used it for this purpose.
I discovered that we have a number of licenses for Sony Vegas and tried using it to pixelate face as per the help pages. It is not particularly intuitive, but I did manage to make some progress. I still have to work out how to get the blurred area to follow the person's face.
In summary, there appears to be a selection of commercial and free software capable of disguising a person in video footage. I suppose the choice comes down to budget and ease of use. With a bit of experience, I think that it would not take too long to do this task in Vegas and I will probably use this as we already have it up and running.
Summary of Responses
Adobe Premier/Elements
I have used Adobe Premiere to black out (not pixellate) a face while preserving the rest of the video. There is a bit of a learning curve to accomplish this, but the final product looks very nice.
Jason Long, Medical College of Wisconsin
I've done this with Adobe Premiere in the past. You can create a circle object, change the alpha value (so the face is kind of visible but not really) and assign motion to it fairly easy. I'm not sure if anything exists that would specifically auto-track the face, but since it is gait it should be a fairly constant movement. You can just assign a start frame position for the circle and an end frame position and it will interpolate the rest of the motion. Premiere has a free 30-day trial, however there are some codec restrictions (Blu-ray, Mpeg, etc).
Ryan Ouckama, McGill University
Have you tried Adobe Premiere Element?
Jessica Yeung
Virtualdub
If you are on PC, I used a lot the Virtualdub software to hide faces in videos.It's free and very efficient.
Baptiste Sandoz
Does the participant's face hold a more or less constant position during the video clip (as in on a treadmill)? If so, I suggest VirtualDub (www.virtualdub.org), a free and fairly powerful software package. Simply download & install it, open the video clip, go to video->filters->add->Logo and select a bmp, jpeg or png of whatever you want over their face (black box, lab logo, smiley face). You can then use the logo dialog box to move the image around the video until it obscures the subject's face. Pick a compression type, save the AVI, and Virtualdub will superimpose the image over that portion of the video, obscuring the subject's face. It's not the "Cops"/news report style pixellation/blur, but it'll easily and completely preserve subject anonymity, and for free.
Henry Astley, Brown University
VideoMach
I like VideoMach for doing this type of thing. It's free if you're ok with having a banner on the first frame. Otherwise you can pay $30 and buy the license. You can't pixelate but you can overlay any jpeg you want on top of the video image at any location...so I just make a jpeg out of a black rectangle and place it over the person's face. I have version 3.5.2...there's probably a newer version out now but this is how I do it:Open the video you want to censor. Then go to the VideoEffect menu and select Add> Overlay> Video Overlay You can now choose any jpeg you want. Just make sure the jpeg is ~100x100 pixels or so otherwise it will be a giant rectangle covering the entire video. Takes a little bit of playing but works well. Let me know if you need more help.
Tilak Dutta, Toronto Rehab
Matlab
I have made a program in Matlab for this. It does not recognize the face however, you have to outline it yourself in the first and last frame, and then the program assumes that the subject walks at a constant speed.
At Hof, University of Groningen
If you happen to have matlab, you may have overlooked it as a possibility you can change each frame using a gaussian blur (or just changing it to a black square, which is easier but less aesthetically pleasing). if the faces move around much that could be a pain, and you'd probably have to write yourself a gui to let you click where it is every few frames, and interpolate the positions.
Otherwise, pinnacle studio will let you do it but it's not free.
Alistair Templeton
ImageJ
I don't know if it does pixelating, but ImageJ is a free video-editing software package. It has a lot of features and a lot of online users, so if you can't find the feature yourself, you could probably find someone online who knows if it does that.
Saryn Goldberg, Hofstra University
Dartfish
We are using Dartfish (http://www.dartfish.com/en/software/dartfish-prosuite/index.htm) for capturing Videos for documentation purpose. We also use this software to disguise faces with the tracking functionality. To do this we track a patient's face with a black bar. A big disadvantage is that tracking doesn't work very well and you have to correct the position of the bar manually. In some cases it is a lot of work.
Daniel Heitzmann, Heidelberg / Germany
Among the community the Adobe Premier products seem to be popular. Among the free software Virtualdub and VideoMach are recommended. Although I hadn't thought about it myself, those with a bit of knowledge of Matlab have used it for this purpose.
I discovered that we have a number of licenses for Sony Vegas and tried using it to pixelate face as per the help pages. It is not particularly intuitive, but I did manage to make some progress. I still have to work out how to get the blurred area to follow the person's face.
In summary, there appears to be a selection of commercial and free software capable of disguising a person in video footage. I suppose the choice comes down to budget and ease of use. With a bit of experience, I think that it would not take too long to do this task in Vegas and I will probably use this as we already have it up and running.
Summary of Responses
Adobe Premier/Elements
I have used Adobe Premiere to black out (not pixellate) a face while preserving the rest of the video. There is a bit of a learning curve to accomplish this, but the final product looks very nice.
Jason Long, Medical College of Wisconsin
I've done this with Adobe Premiere in the past. You can create a circle object, change the alpha value (so the face is kind of visible but not really) and assign motion to it fairly easy. I'm not sure if anything exists that would specifically auto-track the face, but since it is gait it should be a fairly constant movement. You can just assign a start frame position for the circle and an end frame position and it will interpolate the rest of the motion. Premiere has a free 30-day trial, however there are some codec restrictions (Blu-ray, Mpeg, etc).
Ryan Ouckama, McGill University
Have you tried Adobe Premiere Element?
Jessica Yeung
Virtualdub
If you are on PC, I used a lot the Virtualdub software to hide faces in videos.It's free and very efficient.
Baptiste Sandoz
Does the participant's face hold a more or less constant position during the video clip (as in on a treadmill)? If so, I suggest VirtualDub (www.virtualdub.org), a free and fairly powerful software package. Simply download & install it, open the video clip, go to video->filters->add->Logo and select a bmp, jpeg or png of whatever you want over their face (black box, lab logo, smiley face). You can then use the logo dialog box to move the image around the video until it obscures the subject's face. Pick a compression type, save the AVI, and Virtualdub will superimpose the image over that portion of the video, obscuring the subject's face. It's not the "Cops"/news report style pixellation/blur, but it'll easily and completely preserve subject anonymity, and for free.
Henry Astley, Brown University
VideoMach
I like VideoMach for doing this type of thing. It's free if you're ok with having a banner on the first frame. Otherwise you can pay $30 and buy the license. You can't pixelate but you can overlay any jpeg you want on top of the video image at any location...so I just make a jpeg out of a black rectangle and place it over the person's face. I have version 3.5.2...there's probably a newer version out now but this is how I do it:Open the video you want to censor. Then go to the VideoEffect menu and select Add> Overlay> Video Overlay You can now choose any jpeg you want. Just make sure the jpeg is ~100x100 pixels or so otherwise it will be a giant rectangle covering the entire video. Takes a little bit of playing but works well. Let me know if you need more help.
Tilak Dutta, Toronto Rehab
Matlab
I have made a program in Matlab for this. It does not recognize the face however, you have to outline it yourself in the first and last frame, and then the program assumes that the subject walks at a constant speed.
At Hof, University of Groningen
If you happen to have matlab, you may have overlooked it as a possibility you can change each frame using a gaussian blur (or just changing it to a black square, which is easier but less aesthetically pleasing). if the faces move around much that could be a pain, and you'd probably have to write yourself a gui to let you click where it is every few frames, and interpolate the positions.
Otherwise, pinnacle studio will let you do it but it's not free.
Alistair Templeton
ImageJ
I don't know if it does pixelating, but ImageJ is a free video-editing software package. It has a lot of features and a lot of online users, so if you can't find the feature yourself, you could probably find someone online who knows if it does that.
Saryn Goldberg, Hofstra University
Dartfish
We are using Dartfish (http://www.dartfish.com/en/software/dartfish-prosuite/index.htm) for capturing Videos for documentation purpose. We also use this software to disguise faces with the tracking functionality. To do this we track a patient's face with a black bar. A big disadvantage is that tracking doesn't work very well and you have to correct the position of the bar manually. In some cases it is a lot of work.
Daniel Heitzmann, Heidelberg / Germany