Hi Bianca
can you run tksurfer with -reassign, then save the label?
cheers Bruce
On Mon, 29 Jul 2013, Bianca van Kemenade wrote:
Hi, I was wondering whether anyone would still have a tip for this problem?
So far I'm just using " tksurfer P2_BK lh inflated -reassign" and loading the labels on it in one window, and displaying my functional eccentricity data with "tksurfer-sess ....." in a new window. I can sort of draw V3A on the functional data by closely looking at the other window to see where my previously defined V3 is, but it would be great if I could actually load my previously defined labels on the functional data instead.
Thanks! Bianca
On Tue, Jul 16, 2013 at 10:35 AM, Bianca van Kemenade biancavankemenade@gmail.com wrote: I did, but I only managed to get the labels to be displayed correctly when using tksurfer P2_BK lh inflated -reassign and loading the labels on it. When I want to display my eccentricity data with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK and load the labels, the labels are wrong again.
On Mon, Jul 15, 2013 at 11:19 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Can you re-run recon-all on the polar anatomical? doug
On 07/15/2013 05:01 PM, Bianca van Kemenade wrote: > By that I mean that I only have a normal MPRAGE anatomical scan. By > "inflated" I mean that I ran recon-all on this anatomical so that I > can display the inflated surface for example. So when I said I > inflated the anatomical I meant I ran recon-all. Sorry for the > confusing terminology. > > > On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does that mean? doug
On 07/14/2013 09:52 AM, Bianca van Kemenade wrote: > Dear Doug & Bruce, > > It's indeed a confusing situation. What it boils down to is: > > - I scanned the polar angle session and the eccentricity session on > different days > - I had defined V1-3 already based on the polar angle session before > scanning eccentricity > - All data from the polar angle session were lost, apart from the V1-3 > labels I made and the anatomical (not inflated) > - Since I now didn't have an inflated brain anymore, I inflated the > anatomical from the eccentricity > - When I tried to overlay the labels onto this newly inflated brain, > the labels were not correctly displayed > > I just tried again by inflating the anatomical from the polar angle > session (instead of eccentricity), and when I use tksurfer P2_BK lh > inflated -reassign the labels are displayed correctly, so that's great > news! > > However, when I display my eccentricity data, with tksurfer-sess -c > eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are > wrong again. Adding -reassign doesn't work in this command (flag not > recognised). So at least I could open two terminals, one to display > the inflated brain with correct labels, and one to display the > eccentricity data. This is of course not ideal if I want to draw > labels on the eccentricity screen using the labels displayed in the > other screen as a boundary. So if anyone has an idea how to get the > labels to be displayed correctly with the tksurfer-sess command please > let me know. > > In any case, thank you all for your help so far! > > Best, > Bianca > > > > > On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Bianca, I'm still unclear what it is you have done. > > You only need to run freesurfer on one of the anatomicals, it does not > matter which one. > > You should not do anything to the fMRI runs (eg, align with SPM). You > should put your eccen and polar data into a single bold folder under > your session folder. > > Then run preproc-sess. > > I'm not sure how this overlaps with what you have done > > doug > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > 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 > > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 > > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@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 mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. 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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
-- 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/