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 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 the same 
> thing in all subjects, while respecting the individual coordinates). I think 
> my command did this but did not take the c_ras offset into account.
> Is there a better way to do this.
> 
> Thank you  very much,
> Franz
> 
> Am 29.08.2013 um 20:54 schrieb Douglas N Greve:
> 
>> 
>> 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 
>> coorindates don't change at all. It is surprising that they are as close 
>> as they are. What are you trying to do?
>> 
>> doug
>> 
>> 
>> On 08/29/2013 07:41 AM, Franz Liem wrote:
>>> 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). 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 systematically shifted (see figure). 
>>>> Also the newly generated surface does not contain valid geomery 
>>>> information (see mris_info print of lh.white and lh.white.ico6). Is there 
>>>> a way to fix this?
>>>> 
>>>> Another question: is there a reason why mris_decimate is not included in 
>>>> the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build
>>>> 
>>>> Any help is very much appreciated.
>>>> Best, Franz
>>>> 
>>>> 
>>>> mris_info $s/surf/lh.white
>>>>> SURFACE INFO ========================================
>>>>> type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
>>>>> num vertices: 118611
>>>>> num faces   : 237218
>>>>> num strips  : 0
>>>>> surface area: 77595.6
>>>>> AvgVtxArea       0.654202
>>>>> AvgVtxDist       0.885026
>>>>> StdVtxDist       0.251941
>>>>> ctr         : (-33.3535, -11.9536, 42.7693)
>>>>> vertex locs : surfaceRAS
>>>>> talairch.xfm:
>>>>> 1.045  -0.093  -0.014   1.081;
>>>>> 0.099   1.095   0.070  -4.263;
>>>>> 0.010  -0.083   1.290  -41.092;
>>>>> 0.000   0.000   0.000   1.000;
>>>>> surfaceRAS to talaraiched surfaceRAS:
>>>>> 1.045  -0.093  -0.014   1.177;
>>>>> 0.099   1.095   0.070   13.377;
>>>>> 0.010  -0.083   1.290  -49.756;
>>>>> 0.000   0.000   0.000   1.000;
>>>>> talairached surfaceRAS to surfaceRAS:
>>>>> 0.949   0.081   0.006  -1.900;
>>>>> -0.085   0.902  -0.050  -14.449;
>>>>> -0.013   0.058   0.772   37.650;
>>>>> 0.000   0.000   0.000   1.000;
>>>>> volume geometry:
>>>>> extent  : (256, 256, 256)
>>>>> voxel   : ( 1.0000,  1.0000,  1.0000)
>>>>> x_(ras) : (-1.0000, -0.0000,  0.0000)
>>>>> y_(ras) : (-0.0000,  0.0000, -1.0000)
>>>>> z_(ras) : ( 0.0000,  1.0000, -0.0000)
>>>>> c_(ras) : ( 0.0989,  0.9660,  0.9027)
>>>>> ...
>>>> 
>>>> 
>>>> mris_info lh.white.ico6
>>>>> SURFACE INFO ========================================
>>>>> type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
>>>>> num vertices: 40962
>>>>> num faces   : 81920
>>>>> num strips  : 0
>>>>> surface area: 75477.4
>>>>> AvgVtxArea       1.842620
>>>>> AvgVtxDist       1.573724
>>>>> StdVtxDist       0.523314
>>>>> ctr         : (-33.3983, -12.0872, 42.7743)
>>>>> vertex locs : surfaceRAS
>>>>> volume geometry info is either not contained or not valid.
>>>>> ...
>>>> <surfPics.png>_______________________________________________
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>> 
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>> 
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> 
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