Well the situation is as follows: I had a polar angle session, of which I only have the labels and the anatomical (not inflated) left due to a computer crash. In a different session, I scanned both my main experiment and the eccentricity runs. Since the eccentricity was in the same session as the main experiment, I included those runs in my preprocessing batch in SPM, that is I realigned them and coregistered the data to the anatomical of the polar angle session. I then inflated the anatomical of this newer session (the one with eccentricity) and did my analyses of the eccentricity data without using preproc-sess. Apologies if I wasn't clear.
I thought it should therefore be no problem to overlay the polar angle labels onto the newly inflated anatomical, since this one was coregistered to the one from the polar angle session. However the labels don't look correct. Should I have inflated the 'old' anatomical instead? Or would I then nevertheless have needed some kind of transformation? I tried mri_label2label, but when I use a command like this: mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume then it requires access to the anatomical in mri/orig from the srcsubject (the same subject, old session), which I don't have. Well I do have the .nii anatomical, but it can't read that header either, it probably needs the .mgz one which I don't have. When I try the command like this: mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume it does create a new label, which however looks exactly the same as the previous one. When I change --regmethod to surface, it gives this error: ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. I'm not sure about using bbregister for the labels, what would be the movable volume? And do I then use the register.dat file to load the labels with? Thanks again for your patience and help. Best, Bianca On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > Hi Bianca, I'm a little confused. What do you mean you registered with > SPM beforehand? If you're using FSFAST, then the registration is done as > part of preproc-sess. The results for both sessions are on the surface, > so there is no need to do anything to a label created from one session > to show it on another session. > > doug > > > > > On 07/10/2013 11:55 AM, 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 <mailto: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 . 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/ > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- 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/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
