Hi Frederic, Go to your caret distribution directory (e.g., /usr/local/caret or /Applications/caret), and from there cd data_files/fmri_mapping_files. There you will find many target surfaces the Caret mapper uses as a mapping substrate, e.g.:
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_MRITOTAL.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM5.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM95.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM96.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM99.clean.73730.coord These are all the MNI favors, which are described here: http://brainvis.wustl.edu/help/pals_volume_normalization/ You can copy any of these (or their LEFT counterparts) to some other directory, and then run something like this to convert the format to ASCII, which might make it easier to work with other applications: caret_command -file-convert -format-convert ASCII Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord If you are using fnirt on the data with which you want to use the surface, you might consider switching from PALS-B12 to the Conte69 atlas on the fs_LR mesh, described here: http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas Cheers, Donna On Dec 12, 2012, at 4:07 AM, Frederic Roux <[email protected]> wrote: > Dear Donna, Dear Colin, > > thank you for your responses. > > Do you know where I could find the MNI coordinates > of the PALS B12 surface ? > > Best, Frederic > > > Frédéric Roux > Postdoctoral Researcher > www.bcbl.eu > > ----- Original Message ----- > From: "Donna Dierker" <[email protected]> > To: "and SuMS software users Caret SureFit" <[email protected]> > Sent: Friday, December 7, 2012 8:13:32 PM > Subject: [caret-users] Matlab code to read PALS-B12 surface > > > > Passing on Colin's thoughts on matlab. > > > Begin forwarded message: > > > > > From: Colin Reveley < [email protected] > > > Subject: Forward to list > > Date: December 7, 2012 12:34:38 PM CST > > > I can't figure out how to use my iPad to send to the list. Could you pleas > forward: > > > Tim: thanks. That sounds like a confusing problem averted before it > happenned. > > > Frederick: > > > I do not use pals. However any caret surface can be converted to a surf.gii > (no topo). I think caret5 does it. Nearly certain. Although it can't read > that . The workbench beta can do it for sure. > > > Then all metric data can be converted to gifti surfaces (eg func.gii). And so > on. > > > There is a matlab gifti package. It is good. I have used it. I recommend it. > It is what you want. > > > Other people will know more about what can and cannot be made gifti. If its a > paint or metric or surface etc you can do it easily. Although in matlab > obviously mapping the colours is up to you. That might make paints hard. > > > There is cifti. No idea. Someone else may care to comment. > > > I like to use this method for certain displays and analyses, it's good. Pals > is probably partly doable. Look at using matlab, caret and workbench all > together. Actually you just said you were new so this is a bit much. > > > Your surfaces and metrics can be saved in this way using caret5 GUI I believe > . It's not the most introductory thing to want to do however. But surfaces > metrics and paints shouldnt be too bad to get into matlab. obviously you need > the gifti package from matlab exchange. you might consider that caret is > really very good and may very well do what you want. Good luck > > > Colin > > > The reason I sometimes send from [email protected] instead of > [email protected] is that my work SMTP server won't let me send > outside the subnet using the Mac mail client. It works fine via Squirrelmail, > and maybe it would work if I VPN'd in. I am subscribed under both addresses, > though. > > > If you send from an account other than the one under which you are subscribed > to caret-users, or if there are issues with the outgoing mail server, > caret-users will discard your message, thinking you are a spammer. > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
