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 <fis...@nmr.mgh.harvard.edu>
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
<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
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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/
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