So I was looking into mri_label2label and it suggests you can map a label to talairach by using --trgsubject talairach, which I thought may be good to do as a test, creating a label I already have in talairach space, then doing the back transformation you suggested. However, when I tried to do this, I ran across 2 problems. 1) it appears you can't register a subject label to talairach in surface space (ie. --regmethod surface), is this correct? and 2) when I tried to do it in volume, it gave me the error: "Cannot find subject talairach in <my subject directory>". I have the fsaverage brain in there, but is there a talairach brain I need to download as well?
Katie On Mon, Sep 17, 2012 at 1:25 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Katie > > if you set the vertex numbers to -1 then tksurfer will search for the > closest vertex to each point and fill them in. So start with a list of tal > points (and -1 for the vertex), then use mri_label2label to map them to the > individual subject space and visualize it in tkmedit or freeview to make > sure it is right. Then load it into tksurfer, which will assign vertex #s > to each point, after which you can save the label again to make them > permanent. > > > cheers > Bruce > > > On Mon, 17 Sep 2012, Katie Bettencourt wrote: > > 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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