Hi Bruce, So my understanding of the label file is that it has a list of the # of vertices in the label, then each line is the vertex number followed by the RAS coordinates and then some 5th column. I think you are saying that I could use my text file of talairach coordinates (with each line as a new coordinate) like a label file for the talairach brain (is this different from the fsaverage brain?). However, I'm not exactly how to create that sort of file from a list of talairach points since I don't have the vertex number for each coordinate. Am I misunderstanding something?
Is there someway to do some sort of scripting where I create a label from the vertex selected by select_talairach_point using the first talairach point I have and then repeatedly use select_talairach point to load each talairach point onto a subject, then add that point to the label file? I don't quite understand all the tcl commands to understand if this is possible. In then end, our issue is that we seem to be getting different results between freesurfer and brain voyager from identical data analyzed in a ROI defined off of identical data in identical subjects (ie. we take data set 1, define a ROI in FS and BV, then take data set 2, analyzed the response in the ROI, and get different results). We aren't sure why we are getting different results and so wanted to check on where the ROIs were located in relation to each other. Since there doesn't seem to be a way to load BV ROIs into FS, we were trying to work around it by using what we can get out of BV that should be transferrable, the talairach coordinates). Unfortunately, we have to cross platforms like this because historically the data has been done in BV and has produced consistent, published results, but we need to use FS's retinotopic analysis capabilities for future work, but aren't getting the same results on these ROIs and can't figure out why, or even begin to understand it until we can examine whether we are in the same brain space for our ROIs. Thanks, Katie On Mon, Sep 17, 2012 at 12:14 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Katie > > you might be able to create a label file with the tal coords, then use > mri_label2label to map it from tal to the individual subject, then load it > in tksurfer which will map it to the surface. It will probably look spotty > though. > > cheers > Bruce > > > > On Mon, 17 Sep 2012, Katie Bettencourt wrote: > > I'm still trying to figure out a way to display an ROI made elsewhere on >> my >> freesurfer data. I can get all ROI I need in freesurfer in talairach >> points >> (ie. a list of talairach points that cover the entirety of the ROI space), >> but as far as I can see, I can only load one talairach point at a time >> (using select_talairach_point), and then the last point is lost with each >> subsequent call. >> What I really want to do is select a region on the surface that covers a >> set >> of talairach coordinates (instead of say, dilating from 1 talairach >> point). >> Is there any way to do this? Should I use something like the talairach >> transform file to change it into surface coordinates and load those like a >> label somehow, or is there some other way? >> >> Katie >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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