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, M_surf2ras]=mris_read_surface( 'lh.white.ico5');
>
> M_surf2ras = eye(4);
> surf_struct.M_surf2ras = eye(4);
> surf_struct.vertices_trk= surf_struct.vertices ;
> surf_struct.tags(strfind(surf_struct.tags,'cras'):end) = '';
> surf_struct.tags = [surf_struct.tags, sprintf('cras = %2.15e %2.15e
> %2.15e', [0 0 0])];
>
> mris_save_surface('lh.white.ico5.noOffset', surf_struct, M_surf2ras);
Am 02.09.2013 um 21:43 schrieb Douglas Greve:
>
> 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
>> (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,
>>>>
>>>> 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 the c_ras offset, but that did not
>>>> work.
>>>>
>>>> Thanks,
>>>> Franz
>>>>
>>>> Am 30.08.2013 um 17:41 schrieb Douglas N Greve:
>>>>
>>>>> 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 03:51 AM, Franz Liem wrote:
>>>>>> 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>_______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The information in this e-mail is intended only for the person to
>>>>>>>>> whom it is
>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>>>>> the e-mail
>>>>>>>>> contains patient information, please contact the Partners Compliance
>>>>>>>>> HelpLine at
>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>>> you in error
>>>>>>>>> but does not contain patient information, please contact the sender
>>>>>>>>> and properly
>>>>>>>>> dispose of the e-mail.
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> 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/
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>> --
>>>>> 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/
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> _______________________________________________
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
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>>
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>>
>>
>
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