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Dear Prof. Fischl,
Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize.
bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150
Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Hi Debby
you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks
cheers Bruce
On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear all, I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my other images. I have a .nii file of the electric field distribution, registered to T1, representing field strengths in every voxel. Visualization in freeview looks okay, but visualization using tksurfer does not really give the right results (most of the brain is yellow... no field distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how to accomplish this? Thank you very much in advance. Best, Debby
Did you look at the results of the registration to make sure that they are ok? But you probably don't need to run the registration anyway since the surfaces are in the T1.mgz space anyway. How are you verifying that the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and 256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info --vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii
On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear Prof. Fischl,
Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize.
bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150
Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Hi Debby
you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks
cheers Bruce
On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear all, I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my other images. I have a .nii file of the electric field distribution, registered to T1, representing field strengths in every voxel. Visualization in freeview looks okay, but visualization using tksurfer does not really give the right results (most of the brain is yellow... no field distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how to accomplish this? Thank you very much in advance. Best, Debby
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yes, I made a (pretty stupid) mistake in the coregistration. The overlay is working perfectly now. Only for the visualization, is it possible to set my colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' color bars for positive (red) and negative (blue) values? Thank you in advance. Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas Greve [dgreve@mgh.harvard.edu] Verzonden: maandag 17 september 2018 17:04 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Did you look at the results of the registration to make sure that they are ok? But you probably don't need to run the registration anyway since the surfaces are in the T1.mgz space anyway. How are you verifying that the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and 256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info --vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii
On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear Prof. Fischl,
Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize.
bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150
Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Hi Debby
you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks
cheers Bruce
On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear all, I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my other images. I have a .nii file of the electric field distribution, registered to T1, representing field strengths in every voxel. Visualization in freeview looks okay, but visualization using tksurfer does not really give the right results (most of the brain is yellow... no field distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how to accomplish this? Thank you very much in advance. Best, Debby
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.
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Ah, I see now that my configure screen is clipped, so I can click on all the options but I cannot actually apply them... What are the options for -colortable? If I have those, I can play with the visualization from the command line but I cannot find them. Thank you in advance. Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Meusen - Klooster, D.C.W. [D.C.W.Klooster@tue.nl] Verzonden: dinsdag 2 oktober 2018 17:37 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
External Email - Use Caution
Yes, I made a (pretty stupid) mistake in the coregistration. The overlay is working perfectly now. Only for the visualization, is it possible to set my colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' color bars for positive (red) and negative (blue) values? Thank you in advance. Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas Greve [dgreve@mgh.harvard.edu] Verzonden: maandag 17 september 2018 17:04 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Did you look at the results of the registration to make sure that they are ok? But you probably don't need to run the registration anyway since the surfaces are in the T1.mgz space anyway. How are you verifying that the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and 256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info --vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii
On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear Prof. Fischl,
Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize.
bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150
Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Hi Debby
you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks
cheers Bruce
On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear all, I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my other images. I have a .nii file of the electric field distribution, registered to T1, representing field strengths in every voxel. Visualization in freeview looks okay, but visualization using tksurfer does not really give the right results (most of the brain is yellow... no field distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how to accomplish this? Thank you very much in advance. Best, Debby
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
there may be a keyboard shortcut for "apply". Maybe return? Can't you resize the window? On Wed, 3 Oct 2018, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionAh, I see now that my configure screen is clipped, so I can click on all the options but I cannot actually apply them... What are the options for -colortable? If I have those, I can play with the visualization from the command line but I cannot find them. Thank you in advance. Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Meusen - Klooster, D.C.W. [D.C.W.Klooster@tue.nl] Verzonden: dinsdag 2 oktober 2018 17:37 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
External Email - Use CautionYes, I made a (pretty stupid) mistake in the coregistration. The overlay is working perfectly now. Only for the visualization, is it possible to set my colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' color bars for positive (red) and negative (blue) values? Thank you in advance. Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas Greve [dgreve@mgh.harvard.edu] Verzonden: maandag 17 september 2018 17:04 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Did you look at the results of the registration to make sure that they are ok? But you probably don't need to run the registration anyway since the surfaces are in the T1.mgz space anyway. How are you verifying that the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and 256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info --vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii
On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear Prof. Fischl,
Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize.
bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1
tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150
Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface
Hi Debby
you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks
cheers Bruce
On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:
External Email - Use CautionDear all, I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my other images. I have a .nii file of the electric field distribution, registered to T1, representing field strengths in every voxel. Visualization in freeview looks okay, but visualization using tksurfer does not really give the right results (most of the brain is yellow... no field distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how to accomplish this? Thank you very much in advance. Best, Debby
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
Meusen - Klooster, D.C.W.