Flag -reassign is unrecognised unfortunately when I add it to the tksurfer-sess command I posted before. I tried it with tksurfer P2_BK rh inflated -reassign, there at least it ran. However if I then use the tksurfer-sess command again and load the labels I can only see that the labels changed a bit, but they are still not correct.
I assumed coregistering the new session to the (not inflated) anatomical used in the old session used to create the labels would suffice, but apparently some other transformation needs to take place. Do you have an idea how to put the label in the same coordinates? Sorry for my basic questions. Best, Bianca On Wed, Jul 10, 2013 at 6:03 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > you can try adding -reassign, but the label must be in the same coords as > the anatomical for this to work. You'll know right away if it did or not > though > > > cheers > Bruce > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > Hi Bruce, >> >> Thank you for your reply. I coregistered the new data beforehand in SPM >> (to the structural of the old session). So I didn't do >> anything to the label. I displayed the structural with tksurfer-sess -c >> eccen -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I >> wanted to display my eccentricity data) and loaded the label just by >> clicking load --> label. Should I add -reassign in this >> tksurfer command, or is there a way to load the label with a command, to >> which I have to add -reassign? >> >> Also, I'm not familiar with freeview, I tried starting it by typing >> 'freeview' but I get the error: freeview.bin: error while >> loading shared libraries libXss.so.1: cannot open shared object file: No >> such file or directory. It doesn't seem to depend on >> which directory I'm in. >> >> Thanks, >> Bianca >> >> >> On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Bianca >> >> how did you coregister the data? Did you map the label so that it >> is in the coords of the new session? If so, try >> specifying -reassign on the tksurfer command line. That will >> discard the vertex indices in the label (which refer to >> the first session surfaces) and reassign vertex numbers from the >> current subject. This will *only* work if the label >> is in the correct coordinate system. You can verify this by loading >> it in freeview on top of the anatomical from the >> new session >> cheers >> Bruce >> >> >> >> On Wed, 10 Jul 2013, Bianca van Kemenade wrote: >> >> Hi Freesurfers, >> >> I have some participants of whom I obtained retinotopic polar >> angle data in a previous session, and >> scanned eccentricity data in >> a later session. I used the polar angle data to define V1-3, >> and would like to display these labels on >> the eccentricity session >> to help me define V3A. >> >> However, when I load my old V1-3 labels onto the inflated >> brain based on the new session the labels look >> very strange. I >> attached a screenshot of what is supposed to be lh dorsal V1, >> as you can see it is scattered all over >> the cortex. When I load >> the .nii based on the label into MRIcron, the ROI looks fine. >> >> Data from the newer session were coregistered to the older >> session, so that can't be the problem. >> >> I looked around on the wiki and found the command >> mri_label2label that seemed useful. However, this >> command needs acces to the >> 'surf' folders of both sessions. Due to a computer crash I >> only have the labels of the previous session, >> not the 'surf' folder. >> Is there a way to display my old labels onto the new session >> without needing access to 'surf'? >> >> Thanks, >> Bianca >> >> >> >> >> >> 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. >> >> >> >> >> -- >> Bianca van Kemenade, MSc >> Doctoral Candidate, Berlin School of Mind and Brain >> >> Klinik für Psychiatrie und Psychotherapie >> Campus Charité Mitte >> Charitéplatz 1 >> 10117 Berlin >> http://www.mind-and-brain.de/ >> >> -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
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