29 Jul
2013
29 Jul
'13
11:25 a.m.
sure, glad it finally worked Bruce On Mon, 29 Jul 2013, Bianca van Kemenade wrote:
Silly that I didn't think of that, that seems to do the trick! Thank you very much!
Best, Bianca
On Mon, Jul 29, 2013 at 5:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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. Greve, Ph.D. > > > MGH-NMR Center > > > 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>>> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <http://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> > > <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 > > > > > > > > > > > > > > > -- > > > 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>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <mailto: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 > <mailto: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 <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/-- 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/