Hi, all,
I am new to FreeSurfer world. I am trying to do the surface-based
registration using FreeSurfer. I found a tool called mris_register,
which is defined as a command registering a surface to an average
surface template(or another single-subject's surface). But I don't
understand how to use
arguments?
Thank you again.
Best,
Xiaojing
2009/10/6 Bruce Fischl
> Hi Xiaojing,
>
> the inputs are an individual subject sphere created with mris_sphere, and
> statistics in an atlas coordinate system, usually stored in a tif file that
> we supply.
>
> cheers,
> B
something different?
>
> doug
>
> Xiaojing Long wrote:
>
>> Hi, all,
>> I am new to FreeSurfer world. I am trying to do the surface-based
>> registration using FreeSurfer. I found a tool called mris_register,
>> which is defined as a command registering a surface t
another, but in our experience using the atlas statistics and the
> measures of cross-subject variability stabilizes the whole procedure
>
> On Tue, 6 Oct 2009, Xiaojing Long wrote:
>
> Hi, Douglas,
>>
>> Thank you so much for your help.
>>
>>
Hi,
I have a question regarding how to average cortical thickness maps.
I have a dataset with 10 MR brain images and I've run recon-all on each
of them. So I've got thickness maps ?h.thickness for each subject. I wonder
whether freesurfer provides a tool that can average the cortical thickness
ma
the subjects?
Thank you.
Best,
Xiaojing
2010/3/17 Bruce Fischl
> Hi Xiaojing,
>
> mris_average_curvature will do it, and I think Doug has some other tools
> that will as well.
>
> cheers,
> Bruce
> On Wed, 17 Mar 2010, Xiaojing Long wrote:
>
> Hi,
>>
&
I would use -o fsaverage, then you can simply load the average
> thickness onto the fsaverage inflated surface.
>
> cheers
> Bruce
>
>
>
> On Thu, 18 Mar 2010, Xiaojing Long wrote:
>
> Hi, Bruce,
>>
>> Thanks a lot for your suggestion.
>>
>>
Hi,
I have a question regarding how to convert a cortical thickness map (i.e.
lh.thickness) to a NIFTY file.
I have a subject called 'subjid' and I run recon-all on it. So I got the
?h.thickness files. Does freesurfer
provide a tool to convert the surface file to a nifty file?
I tried using the
Hi, all,
I have a question regarding how to get the deformation map in surface-based
registration.
I am wanting to use mris_register to align two surfaces. Can I get the
deformation maps
describing the vertex-to-vertex correspondence? How can I get it?
Thanks a lot.
Best,
Xiaojing
_
tween the ?h.sphere.reg and the
> ?h.sphere. I guess you would want to represent them as arcs of great
> circles.
>
> cheers,
> Bruce
>
> On Tue, 18 May 2010, Xiaojing Long wrote:
>
> Hi, all,
>>
>> I have a question regarding how to get the deformation map in
>>
Hi, all,
I have some questions about performing the FDR correction in Qdec.
I ran recon-all on all my subjects, then ran the surface group analysis
following the Qdec tutorial. There are 3 factors in the qdec.table.dat file:
age, gender and diagnosis. In the Design tab of Qdec, I selected the
dis
I tried that. Still no change.
And I tried running Qdec on all of my datasets. The problem occurs on all of
them.
Xiaojing
2010/7/9 Douglas N Greve
> That is strange. Can you change the FDR to something ridiculous like .5 and
> see if that changes things?
>
> Xiaojin
Now it works if I
enter the FDR in the text box -> press Enter -> click on Set Using FDR
Thank you so much.
Best,
Xiaojing
2010/7/9 Douglas N Greve
> That is strange. Can you change the FDR to something ridiculous like .5 and
> see if that changes things?
>
> X
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