I am still having some trouble with this. As a test, used mri_label2label to convert a label I had in freesurfer to the fsaverage brain, as I couldn't get it to covert just to talairach (see my last email, included below as well). Then I removed all the vertex numbers and replaced them with -1. I could not then use mri_label2label to convert using --regmethod surface (gave me a error: there is a vertex in the label that cannot be match to the surface...) and when I tried the volume method it ran, but then loading the label into tksurfer showed that it was really incorrect (several disjointed blobs across the brain instead of one focus label). However, if I first loaded the label file with the -1 for the vertices into the fsaverage brain, it came up correctly, if I then saved it again, and used mri_label2label and --regmethod surface to convert it back to my original subject brain, it ended up being very close to the original label it was made from.
So, my questions are: 1). Should I be using the fsaverage brain for the talairach coordinates I get from Brain Voyager, even though my understanding was that the fsaverage brain was MNI not talairach? 2). Do I need to bring the label up on the fsaverage brain and save it before converting it to the appropriate subject? Or should it work without this intermediate step? 3). What is the difference between regmethod volume and regmethod surface and why does this cause me to get very different results? Is there something I need to do to the volume method ones to display them on the surface? Thanks, Katie On Tue, Sep 18, 2012 at 12:48 PM, Katie Bettencourt <k...@wjh.harvard.edu>wrote: > 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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