Hey, bruce.Thanks for your help.
According to your suggestion, I use the following command to map each
subject to default fsaverage successfully.
for lh.pial
mri_surf2surf --s chenlingfeng_64 --hemi lh --sval-xyz pial --tval
3D_chenlingfeng_64_to_avg_lh.pial --tval-xyz --trgsubject fsaverage
for lh.thickness
mri_surf2surf --srcsubject chenlingfeng_64 --hemi lh --srcsurfval thickness
--src_type curv --trgsubject avgsubject_3D --trgsurfval
3D_chenlingfeng_64toavg_lh.thickness --trg_type curv
However, the output of SurfStatMaskCut in surfstat seem a bit weird, which
excludes too much non-inter-hemispheric region (see the attached figure 1)
.
So I use make_average_surface to create the customer average of our dataset.
Then to obtain the mask form it again. The problem happens again (see the
attached figure 2).
The SurfStatMaskCut in surfstat said as follows.
Usage: mask = SurfStatMaskCut( surf );
surf.coord = 3 x v matrix of surface coordinates, v=#vertices.
mask = 1 x v vector, 1=inside, 0=outside, v=#vertices.
It looks in -50<y<50 and -20<z<40, and mask vertices where |x|>thresh,
where thresh = 1.5 x arg max of a histogram of |x|.
If is it caused by using different coordinate systems between freesurfer and
surfstat. Or it's not a good idea to perform the statistical analysis of
freesurfer surface data using surfstat?
Any suggestion is appreciated.
Regards,
--
Meng
Lab of Complex System and Artificial Intelligence,
Institute of Automation,Chinese Academy of Sciences(CASIA)
Beijing, 100190,P.R.CHINA
On Mon, Jan 4, 2010 at 10:55 AM, Bruce Fischl
fischl@nmr.mgh.harvard.eduwrote:
> Hi Meng,
>
> you need to use mri_surf2surf to map all your subjects into a common (same
> # of vertices!) space first. We typically use fsaverage for this as the
> target.
>
> cheers,
> Bruce
>
> On Mon, 4 Jan 2010, leemon albert wrote:
>
> Hey.
>>
>> The invidual Freesurfer surface and thickness file can be loaded into
>> surfstat correctly. But the number of vertex varied a bit among subjects
>> in
>> Freesurfer. So when performing the surfstat analysis, I always met the
>> error as follows. I am very curious how to fix it?
>> Thank you in advance.
>>
>> avsurf = SurfStatAvSurf( filesboth );
>> 36 x 2 files to read, % remaining: 100 ??? Error using ==> plus
>> Matrix dimensions must agree.
>>
>> Error in ==> SurfStatAvSurf at 36
>> surf.coord=fun(surf.coord,double(s.coord));
>>
>> SurfStatReadSurf(filesboth(1,:))
>>>>
>>> ans =
>> tri: [598010x3 int32]
>> coord: [3x299009 double]
>>
>>> SurfStatReadSurf(filesboth(2,:))
>>>>
>>> ans =
>> tri: [621056x3 int32]
>> coord: [3x310532 double]
>>
>>> SurfStatReadSurf(filesboth(3,:))
>>>>
>>> ans =
>> tri: [518412x3 int32]
>> coord: [3x259210 double]
>>
>>
>> Best wishes,
>>
>>
--
Meng
Lab of Complex System and Artificial Intelligence,
Institute of Automation,Chinese Academy of Sciences(CASIA)
Beijing, 100190,P.R.CHINA
