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.

---

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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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 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>_______________________________________________ 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.

---

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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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 greve@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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---

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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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 greve@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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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 > greve@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 greve@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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