Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/)
however, I get an error message from matlab:
>>>>>
??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']);
>>>>>>>>>
Am I missing something? Is there anything special with the .gii file form FS?
here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version.
Any help is appreciated!
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for you. It's built for Centos 6, so if you need it for another platform, let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/)
however, I get an error message from matlab:
>>>>>>
??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']);
>>>>>>>>>>
Am I missing something? Is there anything special with the .gii file form FS?
here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version.
Any help is appreciated! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
I have used the command "label2surf", Part of FSL (build 504). (and I have used the "new" gifti lh.white created with your updated version as the input surface)
However, the output gifti does not open in matlab (instead shows the same error message seen before).
Now I would guess that whatever changes you made to mris_convert would have to be applied to "label2surf" as well. I have noticed some changes in the gifti files with your new mris_convert command. However, I'm not so familiar with the gifti file structure.
Maybe I could ask you to have a look into this?
Also, If there is a easier way to achieve my goal any advise is welcome!
Again, many thanks for your efforts so far! Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for you. It's built for Centos 6, so if you need it for another platform, let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/)
however, I get an error message from matlab:
>>>>>>>
??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']);
>>>>>>>>>>>
Am I missing something? Is there anything special with the .gii file form FS?
here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version.
Any help is appreciated! _______________________________________________ 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
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.
Hi Bastian
do you mean a surface that is only a piece of th original surface? You can use label2patch for that, but I'm not sure if we can convert patches to gifti. You should ask the FSL crew about label2surf though - we can't help with that.
cheers Bruce
On Thu, 29 May 2014, Bastian Cheng wrote:
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
I have used the command "label2surf", Part of FSL (build 504). (and I have used the "new" gifti lh.white created with your updated version as the input surface)
However, the output gifti does not open in matlab (instead shows the same error message seen before).
Now I would guess that whatever changes you made to mris_convert would have to be applied to "label2surf" as well. I have noticed some changes in the gifti files with your new mris_convert command. However, I'm not so familiar with the gifti file structure.
Maybe I could ask you to have a look into this?
Also, If there is a easier way to achieve my goal any advise is welcome!
Again, many thanks for your efforts so far! Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for you. It's built for Centos 6, so if you need it for another platform, let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/)
however, I get an error message from matlab:
>>>>>>>>
??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']);
>>>>>>>>>>>>
Am I missing something? Is there anything special with the .gii file form FS?
here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version.
Any help is appreciated! _______________________________________________ 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
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
Hi,
Ok, thank you!
One additional follow up:
Once I converted the lh.white (freesurfer) to the lh.white.gii (gifti), the converted surface (.gii) does not fit on the structural scan from freesurfer anymore (neither brain.mgz or orig.mgz or nu.omz).
How can I register my freesurfer structural data to the new gifti surface?
I have noticed that a transformation matrix is inserted in the gifti file, but have not figured out in which space the image is transformed to..
maybe you could help me clarify that.
Best, Bastian.
On 29 May 2014 17:25, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Bastian
do you mean a surface that is only a piece of th original surface? You can use label2patch for that, but I'm not sure if we can convert patches to gifti. You should ask the FSL crew about label2surf though - we can't help with that.
cheers Bruce
On Thu, 29 May 2014, Bastian Cheng wrote:
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
I have used the command "label2surf", Part of FSL (build 504). (and I have used the "new" gifti lh.white created with your updated version as the input surface)
However, the output gifti does not open in matlab (instead shows the same error message seen before).
Now I would guess that whatever changes you made to mris_convert would have to be applied to "label2surf" as well. I have noticed some changes in the gifti files with your new mris_convert command. However, I'm not so familiar with the gifti file structure.
Maybe I could ask you to have a look into this?
Also, If there is a easier way to achieve my goal any advise is welcome!
Again, many thanks for your efforts so far! Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for you. It's built for Centos 6, so if you need it for another platform, let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/)
however, I get an error message from matlab:
>>>>>>>>>
??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']);
>>>>>>>>>>>>>
Am I missing something? Is there anything special with the .gii file form FS?
here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version.
Any help is appreciated! _______________________________________________ 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bastian,
Are you using freeview to display the surface? If so, you will need to get the newest freeview.bin, which is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
this has been updated to read the new volume geometry info now included in the lh.white.gii file, so that it aligns with the volume (via the c_ras info).
Nick
On Mon, 2014-06-02 at 12:10 +0200, Bastian Cheng wrote:
Hi,
Ok, thank you!
One additional follow up:
Once I converted the lh.white (freesurfer) to the lh.white.gii (gifti), the converted surface (.gii) does not fit on the structural scan from freesurfer anymore (neither brain.mgz or orig.mgz or nu.omz).
How can I register my freesurfer structural data to the new gifti surface?
I have noticed that a transformation matrix is inserted in the gifti file, but have not figured out in which space the image is transformed to..
maybe you could help me clarify that.
Best, Bastian.
On 29 May 2014 17:25, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Bastian
do you mean a surface that is only a piece of th original surface? You can use label2patch for that, but I'm not sure if we can convert patches to gifti. You should ask the FSL crew about label2surf though - we can't help with that.
cheers Bruce
On Thu, 29 May 2014, Bastian Cheng wrote:
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
I have used the command "label2surf", Part of FSL (build 504). (and I have used the "new" gifti lh.white created with your updated version as the input surface)
However, the output gifti does not open in matlab (instead shows the same error message seen before).
Now I would guess that whatever changes you made to mris_convert would have to be applied to "label2surf" as well. I have noticed some changes in the gifti files with your new mris_convert command. However, I'm not so familiar with the gifti file structure.
Maybe I could ask you to have a look into this?
Also, If there is a easier way to achieve my goal any advise is welcome!
Again, many thanks for your efforts so far! Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for you. It's built for Centos 6, so if you need it for another platform, let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/)
however, I get an error message from matlab:
>>>>>>>>>>
??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']);
>>>>>>>>>>>>>>
Am I missing something? Is there anything special with the .gii file form FS?
here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version.
Any help is appreciated! _______________________________________________ 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
again thank you your help! That works nicely.
Where to I find the transformation matrix to register my structural volume data to the gii. surface file?
I found two matrices in the lh.white.gii (<MatrixData>), but not sure if it fits.
I have to use the volume scan and gii suface in matlab for localization and source reconstruction of EEG data (that's why I can't use freeview).
Bastian
On 2 June 2014 20:50, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Are you using freeview to display the surface? If so, you will need to get the newest freeview.bin, which is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
this has been updated to read the new volume geometry info now included in the lh.white.gii file, so that it aligns with the volume (via the c_ras info).
Nick
On Mon, 2014-06-02 at 12:10 +0200, Bastian Cheng wrote:
Hi,
Ok, thank you!
One additional follow up:
Once I converted the lh.white (freesurfer) to the lh.white.gii (gifti), the converted surface (.gii) does not fit on the structural scan from freesurfer anymore (neither brain.mgz or orig.mgz or nu.omz).
How can I register my freesurfer structural data to the new gifti surface?
I have noticed that a transformation matrix is inserted in the gifti file, but have not figured out in which space the image is transformed to..
maybe you could help me clarify that.
Best, Bastian.
On 29 May 2014 17:25, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Bastian
do you mean a surface that is only a piece of th original surface? You can use label2patch for that, but I'm not sure if we can convert patches to gifti. You should ask the FSL crew about label2surf though - we can't help with that.
cheers Bruce
On Thu, 29 May 2014, Bastian Cheng wrote:
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
I have used the command "label2surf", Part of FSL (build 504). (and I have used the "new" gifti lh.white created with your updated version as the input surface)
However, the output gifti does not open in matlab (instead shows the same error message seen before).
Now I would guess that whatever changes you made to mris_convert would have to be applied to "label2surf" as well. I have noticed some changes in the gifti files with your new mris_convert command. However, I'm not so familiar with the gifti file structure.
Maybe I could ask you to have a look into this?
Also, If there is a easier way to achieve my goal any advise is welcome!
Again, many thanks for your efforts so far! Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for you. It's built for Centos 6, so if you need it for another platform, let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote:
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/)
however, I get an error message from matlab:
>>>>>>>>>>> ??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']); >>>>>>>>>>>>>>>
Am I missing something? Is there anything special with the .gii file form FS?
here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ
I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version.
Any help is appreciated! _______________________________________________ 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Problem solved!
took some effort trying everything out, but finally found a simple solution by transforming everything into MNI
Here's how to convert from surface RAS to mni305
mni305ras = X*S*inv(K)*ras X = talairach.xfm S = scanner vox2ras (mri_info --vox2ras orig.mgz) K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz) ras = surface ras from gifti file.
found here: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 3 June 2014 09:08, Bastian Cheng bastiancheng@gmail.com wrote:
Hi Nick,
again thank you your help! That works nicely.
Where to I find the transformation matrix to register my structural volume data to the gii. surface file?
I found two matrices in the lh.white.gii (<MatrixData>), but not sure if it fits.
I have to use the volume scan and gii suface in matlab for localization and source reconstruction of EEG data (that's why I can't use freeview).
Bastian
On 2 June 2014 20:50, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Are you using freeview to display the surface? If so, you will need to get the newest freeview.bin, which is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
this has been updated to read the new volume geometry info now included in the lh.white.gii file, so that it aligns with the volume (via the c_ras info).
Nick
On Mon, 2014-06-02 at 12:10 +0200, Bastian Cheng wrote:
Hi,
Ok, thank you!
One additional follow up:
Once I converted the lh.white (freesurfer) to the lh.white.gii (gifti), the converted surface (.gii) does not fit on the structural scan from freesurfer anymore (neither brain.mgz or orig.mgz or nu.omz).
How can I register my freesurfer structural data to the new gifti surface?
I have noticed that a transformation matrix is inserted in the gifti file, but have not figured out in which space the image is transformed to..
maybe you could help me clarify that.
Best, Bastian.
On 29 May 2014 17:25, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Bastian
do you mean a surface that is only a piece of th original surface? You can use label2patch for that, but I'm not sure if we can convert patches to gifti. You should ask the FSL crew about label2surf though - we can't help with that.
cheers Bruce
On Thu, 29 May 2014, Bastian Cheng wrote:
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
I have used the command "label2surf", Part of FSL (build 504). (and I have used the "new" gifti lh.white created with your updated version as the input surface)
However, the output gifti does not open in matlab (instead shows the same error message seen before).
Now I would guess that whatever changes you made to mris_convert would have to be applied to "label2surf" as well. I have noticed some changes in the gifti files with your new mris_convert command. However, I'm not so familiar with the gifti file structure.
Maybe I could ask you to have a look into this?
Also, If there is a easier way to achieve my goal any advise is welcome!
Again, many thanks for your efforts so far! Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for you. It's built for Centos 6, so if you need it for another platform, let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote: > Dear Freesurfer-Experts, > > I would like to create gifti-surfaces to use in matlab. > > That's what I am doing so far (latest FS-Version): > > mris_convert lh.white lh.white.gii > > I then try to open it using the "gifti" command (g=gifti('file.gii')) > (http://www.artefact.tk/software/matlab/gifti/) > > however, I get an error message from matlab: > >>>>>>>>>>>> > ??? Attempt to reference field of non-structure array. > Error in ==> gifti.subsref at 28 > varargout{1} = this.data{j}.space.MatrixData; > Error in ==> gifti.struct at 17 > [values{i,:}] = subsref(this(:), substruct('.',names{i})); > Error in ==> gifti.display at 17 > eval([display_name ' = struct(this);']); >>>>>>>>>>>>>>>> > > Am I missing something? Is there anything special with the .gii file form FS? > > here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ > > I am able to open the gifti file with freeview. > I also updated the gifti-toolbox in matlab to the latest version. > > > Any help is appreciated! > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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Bastion,
Hi, I'm a bit late in this reply. You can use 'mris_info lh.white.gii' to display the matrices in that file. The one labeled 'FS_VOLGEOM_RAS' is the one that will register the surface with the orig.mgz volume file. Note that it will always be three numbers (c_r, c_a, c_s) which just shifts the center of the surface to match the center of the orig volume.
I wouldn't think you would need to use the MNI305 transform, as that's an affine transform to align it in 'talairach' space.
N.
On Thu, 2014-06-05 at 09:35 +0200, Bastian Cheng wrote:
Problem solved!
took some effort trying everything out, but finally found a simple solution by transforming everything into MNI
Here's how to convert from surface RAS to mni305
mni305ras = X*S*inv(K)*ras X = talairach.xfm S = scanner vox2ras (mri_info --vox2ras orig.mgz) K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz) ras = surface ras from gifti file.
found here: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 3 June 2014 09:08, Bastian Cheng bastiancheng@gmail.com wrote:
Hi Nick,
again thank you your help! That works nicely.
Where to I find the transformation matrix to register my structural volume data to the gii. surface file?
I found two matrices in the lh.white.gii (<MatrixData>), but not sure if it fits.
I have to use the volume scan and gii suface in matlab for localization and source reconstruction of EEG data (that's why I can't use freeview).
Bastian
On 2 June 2014 20:50, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote:
Bastian,
Are you using freeview to display the surface? If so, you will need to get the newest freeview.bin, which is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
this has been updated to read the new volume geometry info now included in the lh.white.gii file, so that it aligns with the volume (via the c_ras info).
Nick
On Mon, 2014-06-02 at 12:10 +0200, Bastian Cheng wrote:
Hi,
Ok, thank you!
One additional follow up:
Once I converted the lh.white (freesurfer) to the lh.white.gii (gifti), the converted surface (.gii) does not fit on the structural scan from freesurfer anymore (neither brain.mgz or orig.mgz or nu.omz).
How can I register my freesurfer structural data to the new gifti surface?
I have noticed that a transformation matrix is inserted in the gifti file, but have not figured out in which space the image is transformed to..
maybe you could help me clarify that.
Best, Bastian.
On 29 May 2014 17:25, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Bastian
do you mean a surface that is only a piece of th original surface? You can use label2patch for that, but I'm not sure if we can convert patches to gifti. You should ask the FSL crew about label2surf though - we can't help with that.
cheers Bruce
On Thu, 29 May 2014, Bastian Cheng wrote:
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
I have used the command "label2surf", Part of FSL (build 504). (and I have used the "new" gifti lh.white created with your updated version as the input surface)
However, the output gifti does not open in matlab (instead shows the same error message seen before).
Now I would guess that whatever changes you made to mris_convert would have to be applied to "label2surf" as well. I have noticed some changes in the gifti files with your new mris_convert command. However, I'm not so familiar with the gifti file structure.
Maybe I could ask you to have a look into this?
Also, If there is a easier way to achieve my goal any advise is welcome!
Again, many thanks for your efforts so far! Bastian.
On 29 May 2014 02:05, Nick Schmansky, MGH nicks@nmr.mgh.harvard.edu wrote: > Bastian, > > Hi, I've posted a new mris_convert which should solve the problem for > you. It's built for Centos 6, so if you need it for another platform, > let me know. It's here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ > > Nick > > > > On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote: >> Dear Freesurfer-Experts, >> >> I would like to create gifti-surfaces to use in matlab. >> >> That's what I am doing so far (latest FS-Version): >> >> mris_convert lh.white lh.white.gii >> >> I then try to open it using the "gifti" command (g=gifti('file.gii')) >> (http://www.artefact.tk/software/matlab/gifti/) >> >> however, I get an error message from matlab: >> >>>>>>>>>>>>> >> ??? Attempt to reference field of non-structure array. >> Error in ==> gifti.subsref at 28 >> varargout{1} = this.data{j}.space.MatrixData; >> Error in ==> gifti.struct at 17 >> [values{i,:}] = subsref(this(:), substruct('.',names{i})); >> Error in ==> gifti.display at 17 >> eval([display_name ' = struct(this);']); >>>>>>>>>>>>>>>>> >> >> Am I missing something? Is there anything special with the .gii file form FS? >> >> here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ >> >> I am able to open the gifti file with freeview. >> I also updated the gifti-toolbox in matlab to the latest version. >> >> >> Any help is appreciated! >> _______________________________________________ >> 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 > > > 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
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