Hi Bruce,My problem has been solved. I rotate the ?h.sphere by mris_rotate <source>
0 0 90 <output> and then I used mris_register to register it to
fsaverage and I saw my result is perfectly registered to fsaverage. it means
that mris_register was not able to realign the sphere to fsaverage if
the original orientation is bigger than some degrees like 90.
I don't think you need to spend time on it. thanks alot for your helps.
bests
Rouhi
On Sat, Aug 13, 2011 at 11:09 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
you can either ftp it or put it on our file drop (you can find both on
our wiki)
On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
where can I upload one subject? which I have problem with that subject in
RH registraton.
On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
if the aseg is good I don't see how it's possible that we don't know
about the 90 deg rotation. If you upload the dataset
I'll take a look
On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote:
Hi BruceI think the aseg is good but only rotated 90 degree.
I will try to rotate sphere to see how it will create
sphere.reg.
On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Matt
if they were tipped forward 90deg and we didn't detect it I would
think that the aseg would fail catastrophically. Did that
happen?
Bruce
On Fri, 12 Aug 2011, Matt Glasser wrote:
So I thought the issue had been solved, but perhaps not. Bruce, we
(i.e. David) think the problem with Rouhi?s data is that
FreeSurfer
did not
detect that the original images were tipped forward 90 degrees and
as a result the surface registration failed intermittently
(i.e. in
some
subjects it okay, but in others it is not). These data were created
with a fairly old version of FreeSurfer (Rouhi can give
the version
number),
and then a significant amount of manual effort was put into defining
some retinotopy on the data. Therefore it isn?t really
a feasible
option to
just rerun the data with a newer version of FreeSurfer, but we want
to make use of accurate FreeSurfer surface registration
to make group
average
retinotopy results. So the question is how do we go about making
sure the spheres are initialized to have the correct rigid
orientation
before
the registration proceeds.
Thanks,
Matt.
_________________________________________________________________________________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi
Sent: Friday, August 12, 2011 12:38 PM
To: Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file .
But when I open the new surface like white it was not
rotated.
Is there any special thing that I have to do?
Best
Rouhi
On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi
<roohy...@gmail.com> wrote:
Dear Bruce
If I want to rotate sucli pattern too if it is the same?
On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
I guess you could rotate the surfaces, save them, then resample the
labels so that they get the new surface coords and sample
them into
the
volume, then onto the newly created surfaces. Not sure, we haven't
ever had to do anything like this.
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I think the easiest way is to create all surfaces again but with
corrected
and well aligned brain. The next step for me to create new labels
from old
labels based on white surface (90 degree rotated) to new white
surface. But
how? Is there any way to do that? I mean like label2label or
surf2surf if
two surfaces are the same but one of them only rotated?!
Bests
Rouhi
On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
I don't see how anything would work if it was off by 90deg, but
I guess you should try it
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Because I am using a result from a very old experiment
that done on wrong direction and the orig.mgz s are not
oriented according to
freesurfer template. I cannot creat white because all
results that I have (label files) are on white surface.
The only way that I think I need to
realign all surfaces and volume and apply that rotation on
my label files.
On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
not easily. Why would you need to do such a thing?
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I have a data set which I can not create the white
surfaces because all of my results are according to white
surface. I would
like to know is
there any way to rotate all surfaces and volumes and
labels ... (everything) after finishing recon-all process.
like 90 degree
around X axis?
and apply this rotation to all data set?
Best
Rouhi
On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Rouhi
I don't really understand. Are you saying you
transformed the initial image before giving it to
recon-all? There is a
switch to
mris_register to initialize with the tal xform,
but we never use it as in pretty extensive tests it didn't
seem to help.
mris_register has a very large initial capture
range due to it's global search, so I would be surprised
if the initial
orientation
was the problem.
cheers
Bruce
On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I think I found the problem. The problem came
from the original oriantation of T1 image and I think
mris_register could
not
find it itself during
the recon-all. I added to have initial alignment
to inflated and the problem solved.( mris_register -curve
-inflated
?h.sphere <template
target> ?h.sphere.reg ) I think it is very
important to add it to recon-all because if the user
doesn't know the real
oriantation it might make
such a problem.
Thanks for your quick response.
On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah
Abdollahi <roohy...@gmail.com> wrote:
Dear Bruce
I am working on Freesurfer 2 caret meshes.
I am using FreeSurfer2CaretConvertAndRegisterClean.sh
from Van Essen lab
to
create caret
surfaces. when I look at my subjects'
surfaces I can see in flat map in caret some of subjects
sulci patterns are
really
distorted
and I think it is related to
sphere registration to fsaverage sphere. Beacsue the code
is using sphere.reg to create
all
surfaces.
for the subjects which I have less
distortion on sulci pattern I have good data (3 subjects)
but for the (9
subjects)
rest it seems
they have problem to register to fsaverage.
Is there any way that I can be sure that
sphere.reg properly created?
Thank you very much
Rouhi
On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Try using fsaverage as the trgsubject
Cheers
Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah
Abdollahi <roohy...@gmail.com> wrote:
> .V1_reg.label --regmethod surface
--srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and
when I tried to load
the
output
label file on fsaverage surface like
inflated one it shows a lot of point looks like it is not
deformed properly. Is
it
related
to registration to fsaverage or something
esle? The question is how I can register the subjects
surfaces to fsaverage
surfaces?
-- With Best Regards Rouhi
--0015175120c69a3c6804aa2ffb81 Content-Type: text/html;
charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Dear freesurfer experts
>
> I've tried to export my label file from
individual space to fsaverage space by using this command:
>
> mri_label2label --srclabel rh.V1.label
--srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg.
> like it is not deformed properly.
> Is it related to registration to fsaverage or
something esle?
> The question is how I can register the
subjects surfaces to fsaverage
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--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
--
With Best Regards
Rouhollah Abdollahi
