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
> <mailto:greve@nmr.mgh.harvard.edu> <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:Freesurfer@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>>>> 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
> > >
> > >
> > >
> > >
> > >
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> > >
> > >
> > > --
> > > 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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> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
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> >
> >
> > --
> > 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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> --
> 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>
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>
>
> --
> 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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