Hi Doug,
I found a workaround. I used matlab code from from gradient_nonlin_unwarp to
remove the c_ras offset from the vertex coordinates and set c_ras to 0. Then I
mris_convert the new surface to .gii. This gives me perfectly aligned surfaces.
Thanks for your help,
Franz
> [surf_struct, tags,
This info is probably not stored in the gii header. I'll have to take a
look which could take a while. Depending on what you are doing, it might
not be important.
doug
On 9/2/13 2:58 PM, Franz Liem wrote:
> Hi Doug,
> this gives exactly the same surface as surf2surf followed by mris_convert
>
Hi Doug,
this gives exactly the same surface as surf2surf followed by mris_convert (i.e.
with offset).
Thanks,
Franz
Am 02.09.2013 um 16:50 schrieb Douglas Greve:
>
> What if you specify the output of surf2surf to be a gii file?
>
>
> On 9/2/13 6:47 AM, Franz Liem wrote:
>> Dear Doug,
>>
>>
What if you specify the output of surf2surf to be a gii file?
On 9/2/13 6:47 AM, Franz Liem wrote:
> Dear Doug,
>
> thank you so much, the fix works great.
> The problem now is that when I mris_convert the newly generated surface to
> .gii the volume geometry is lost again and the offset reintr
Dear Doug,
thank you so much, the fix works great.
The problem now is that when I mris_convert the newly generated surface to .gii
the volume geometry is lost again and the offset reintroduced.
Is there a way to fix this? I have tried to give mri_surf2surf a register.dat
that would correct for
Sorry, I'm answering your emails in reverse order. Your command should
do what youwant once you use the new version below
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard
note the --tval-xyz requires an argument (give it the orig.mgz)
doug
On 08/30/2013
Oh, I see. It must be the volume geometry being invalid. When I try it
with the new version of mri_surf2surf, the two surfaces are right on top
of each other.
doug
On 08/30/2013 09:22 AM, Franz Liem wrote:
> Hi again,
> just a clarification. The two surfaces in the image are single subject
>
Hi again,
just a clarification. The two surfaces in the image are single subject surfaces
(the original lh.white and the transformed lh.white.ico6), not fsaverage6
surfs.
Best,
Franz
Am 30.08.2013 um 09:51 schrieb Franz Liem:
> Hi Doug,
>
> thanks a lot.
> I am using Darwin-snowleopard and c
Hi Doug,
thanks a lot.
I am using Darwin-snowleopard and centos6_x86_64.
What I am trying to do is to use the white surface as seed for probtrackx.
Therefore, I would like to reduce the number of vertices and at the same time
bring the surfaces into a common space (so that vertex x is meaning
Hi Franz, I just programmed a fix into mri_surf2surf. What platform do
you use?
As for the shift, you would not expect them to line up. In fact, that
command line does not make a lot of sense. What it is doing is mapping
the xyz coordinates in the native space to a new tesselation. The xyz
co
Dear Freesurfers,
sorry for the bump, but my message seems to have gone unnoticed.
Thanks so much for any ideas.
Franz
Am 22.08.2013 um 13:37 schrieb Franz Liem:
> Dear Freesurfers,
>
> I tried to map a single subject surface to fsaverageX (for the sake of
> demonstration lets take fsaverage6)
Dear Freesurfers,
I tried to map a single subject surface to fsaverageX (for the sake of
demonstration lets take fsaverage6). I did the following:
mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject
fsaverage6 --tval-xyz --tval ./lh.white.ico6
This produces a surface that seems
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