er-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 fsavera
_**
>> __________**__**
>> __
>>
>>
>> From:
>> freesurfer-boun...@nmr.mgh.**harvard.edu[mailto:
>> freesurfer-bounces@**nmr.mgh.harvard.edu]
>> On Behalf Of Rouhollah Abdoll
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
gt;
>>
>> Matt.
>>
>>
>>
>>
>> __**__**
>> __**__**
>> _________
>>
>>
>> From:
>> f
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
.**harvard.edu[mailto:
>> freesurfer-bounces@**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 fsaverag
t: 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 wrote:
n 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
oh, that won't work. That's just for visualization, it doesn't actually
change any coordinates. As I said, we don't usually do this. If you can
come up with a rotation matrix I guess either mri_surf2surf or
mris_transform would work
cheers
Bruce
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
you won't need to rotate them. They are attached to the surface, so if
the surface is rotated, they will be too
On Fri, 12 Aug 2011, Rouhollah
Abdollahi 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
wrote:
I
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 wrote:
> Dear Bruce
> If I want to rotate sucli pattern
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 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
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 an
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? a
Hi Rouhi
you can specify -norot to disable the initial rotation, but I wouldn't
think that would be a good thing to do. To decrease distortion you would
increase the strength of the metric term using -dist . The default
is 5, so you could try raising it to 10 or 15.
cheers
Bruce
On Fri, 12
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 initi
Hi Rouhi
it's hard to tell from looking at the sphere.reg by itself. In general
though if the parcellations are correct then the registration must be
pretty good.
cheers
Bruce
On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce
I checked the parcellation and look quiet OK. I attached
Dear Bruce,
I have two questions.
I saw there are a lot of algorithms for mris_register. Which one are more
precise and has less distortion on sulci pattern?
In initial alignment if I want to rotate the surface with -rotate [ alpha is
(ear to ear) beta(Back to nose) ... ]. Am I right?. and if I wa
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
?h.sphere.re
Try using fsaverage as the trgsubject
Cheers
Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi 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 sh
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.label --regmethod surface
--srcsurfreg sphere --trgsurfreg sphere.reg --hem
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