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
<biancavankemen...@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 <gr...@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
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@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
> > > <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> > <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> <mailto: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>
> > <mailto:fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>>
> > <mailto:fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>
> > <mailto:fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>>>
> > > <mailto:fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>
> > <mailto:fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>>
> > > <mailto:fis...@nmr.mgh.harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>
> > <mailto: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
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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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> > <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
> > > gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
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> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>
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> <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>
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> > >
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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/
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
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> > <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
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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>
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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/
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@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>
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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> _______________________________________________
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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/
>
>
> _______________________________________________
> Freesurfer mailing list
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--
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
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_______________________________________________
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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/
--
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/
