Re: [Freesurfer] displaying labels from old session onto new session

[Bruce Fischl]

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  
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 
 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 
 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
> 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,

Re: [Freesurfer] displaying labels from old session onto new session

[Bruce Fischl]

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 
 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  
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
> 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
>     > 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
>     >     

Re: [Freesurfer] displaying labels from old session onto new session

[Bianca van Kemenade]

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
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
> > 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
> >  

Re: [Freesurfer] displaying labels from old session onto new session

[Bianca van Kemenade]

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
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
> > 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,
> > >
> > > Tha

Re: [Freesurfer] displaying labels from old session onto new session

[Bianca van Kemenade]

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
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
> > 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 fi

Re: [Freesurfer] displaying labels from old session onto new session

[Bruce Fischl]

mri_label2label is what we would typically use. You can probably use 
bbregister to generate the registration from the old session to the new 
anatomicals


On Wed, 10 Jul 2013, Bianca 
van Kemenade wrote:



Flag -reassign is unrecognised unfortunately when I add it to the tksurfer-sess 
command I posted before. I tried it with
tksurfer P2_BK rh inflated -reassign, there at least it ran. However if I then 
use the tksurfer-sess command again and load the
labels I can only see that the labels changed a bit, but they are still not 
correct.

I assumed coregistering the new session to the (not inflated) anatomical used 
in the old session used to create the labels would
suffice, but apparently some other transformation needs to take place. Do you 
have an idea how to put the label in the same
coordinates? Sorry for my basic questions.

Best,
Bianca


On Wed, Jul 10, 2013 at 6:03 PM, Bruce Fischl  
wrote:
  you can try adding -reassign, but the label must be in the same coords as 
the anatomical for this to work. You'll
  know right away if it did or not though

  cheers
  Bruce
  On Wed, 10 Jul 2013, 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 
 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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but does

Re: [Freesurfer] displaying labels from old session onto new session

[Bianca van Kemenade]

Flag -reassign is unrecognised unfortunately when I add it to the
tksurfer-sess command I posted before. I tried it with tksurfer P2_BK rh
inflated -reassign, there at least it ran. However if I then use the
tksurfer-sess command again and load the labels I can only see that the
labels changed a bit, but they are still not correct.

I assumed coregistering the new session to the (not inflated) anatomical
used in the old session used to create the labels would suffice, but
apparently some other transformation needs to take place. Do you have an
idea how to put the label in the same coordinates? Sorry for my basic
questions.

Best,
Bianca


On Wed, Jul 10, 2013 at 6:03 PM, Bruce Fischl wrote:

> you can try adding -reassign, but the label must be in the same coords as
> the anatomical for this to work. You'll know right away if it did or not
> though
>
>
> cheers
> Bruce
> On Wed, 10 Jul 2013, 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 
>> 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/
>>
>>


-- 
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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Re: [Freesurfer] displaying labels from old session onto new session

[Bruce Fischl]

you can try adding -reassign, but the label must be in the same coords as 
the anatomical for this to work. You'll know right away if it did or not 
though


cheers
Bruce
On Wed, 10 Jul 2013, 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  
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/

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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.

Re: [Freesurfer] displaying labels from old session onto new session

[Bianca van Kemenade]

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 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/
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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.

Re: [Freesurfer] displaying labels from old session onto new session

[Bruce Fischl]

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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contains patient information, please contact the Partners Compliance HelpLine at
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