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.eduwrote:
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> 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 doesnot
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 andthe
> 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>>> wrote: > > > Hi Bianca, I'm a little confused. What do you mean you registered with > SPM beforehand? If you're using FSFAST, then the registrationis
> 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>>>> 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, tryspecifying
> > -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>> > > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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/
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