Hi,
I do not have a good understanding of the mri_vol2surf command.
1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh
Thanks, Zhivago...
Hi Zhivago
1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary.
2) The default projfrac, as documented in the -help response, is 0.
3) Yes, 0-->white matter boundary. 1--> pial boundary.
4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface.
cheers Bruce
On Sun, 15 Jan 2017, Zhivago wrote:
Hi,
I do not have a good understanding of the mri_vol2surf command.
- Can this only project the part of the volume that lies between the white
& pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh
Thanks, Zhivago...
Hey Bruce,
Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these.
1) The mri_vol2surf is used to project the activations from the GM onto an inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense?
2) When mri_vol2surf projects a volume to a surface, does it average the activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful.
3) Is mri_vol2surf the only way to view activation maps on inflated surfaces or any surface?
Cheers, Zhivago...
On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Zhivago
- You can project from inside the ?h.white surface if projfrac<0 and
outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary.
The default projfrac, as documented in the -help response, is 0.
Yes, 0-->white matter boundary. 1--> pial boundary.
The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector,
which is a scalar field over the surface.
cheers Bruce
On Sun, 15 Jan 2017, Zhivago wrote:
Hi,
I do not have a good understanding of the mri_vol2surf command.
- Can this only project the part of the volume that lies between the
white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh
Thanks, Zhivago...
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.
1) This is up to you. Jon Polimeni had a nice paper describing the trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface).
2) This is also up to you.Read the help in mri_vol2surf. e.g.:
mri_vol2surf --help . . . --projfrac-avg min max del : average along normal
3) it is the way that we support.
cheers Bruce
On Sun, 15 Jan 2017, Zhivago wrote:
Hey Bruce,
Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these.
- The mri_vol2surf is used to project the activations from the GM onto an
inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense?
- When mri_vol2surf projects a volume to a surface, does it average the
activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful.
- Is mri_vol2surf the only way to view activation maps on inflated surfaces
or any surface?
Cheers, Zhivago...
On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Zhivago
1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago...
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.
Thanks Bruce! Appreciate all the help,
On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
- This is up to you. Jon Polimeni had a nice paper describing the
trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface).
- This is also up to you.Read the help in mri_vol2surf. e.g.:
mri_vol2surf --help . . . --projfrac-avg min max del : average along normal
- it is the way that we support.
cheers Bruce
On Sun, 15 Jan 2017, Zhivago wrote:
Hey Bruce,
Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these.
- The mri_vol2surf is used to project the activations from the GM onto an
inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense?
- When mri_vol2surf projects a volume to a surface, does it average the
activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful.
- Is mri_vol2surf the only way to view activation maps on inflated
surfaces or any surface?
Cheers, Zhivago...
On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Zhivago
1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago...
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
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,
From whatever I read, there seem to be 2 ways for overlaying activation
maps on surfaces.
1) automatic/manual registration of activation volume to orig.mgz and usage of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be overlaid on an inflated surface in freeview or tksurfer using the register.dat.
2) automatic/manual registration of activation volume to orig.mgz and overlay the activation volume on the inflated surface in tksurfer using the register.dat
I want to know if both these are valid methods and if so, what are the pros and cons of each. Seems like mri_vol2surf lets us decide what part of the volume should be projected on the surface using the projfac arguments. But the direct volume overlay in tksurfer doesn't provide that option. In that case what part of the volume is projected on to the surface?
Thanks, Zhivago...
On Sun, Jan 15, 2017 at 10:12 PM, Zhivago zhivagoa@gmail.com wrote:
Thanks Bruce! Appreciate all the help,
On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
- This is up to you. Jon Polimeni had a nice paper describing the
trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface).
- This is also up to you.Read the help in mri_vol2surf. e.g.:
mri_vol2surf --help . . . --projfrac-avg min max del : average along normal
- it is the way that we support.
cheers Bruce
On Sun, 15 Jan 2017, Zhivago wrote:
Hey Bruce,
Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these.
- The mri_vol2surf is used to project the activations from the GM onto
an inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense?
- When mri_vol2surf projects a volume to a surface, does it average the
activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful.
- Is mri_vol2surf the only way to view activation maps on inflated
surfaces or any surface?
Cheers, Zhivago...
On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Zhivago
1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago...
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
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 Zhivago
tksurfer is deprecated and uses one of the methods available in mri_vol2surf, so our advice would be to use vol2surf
cheers Bruce On Wed, 18 Jan 2017, Zhivago wrote:
[cleardot.gif] Hi,
From whatever I read, there seem to be 2 ways for overlaying activation maps on surfaces.
- automatic/manual registration of activation volume to orig.mgz and usage
of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be overlaid on an inflated surface in freeview or tksurfer using the register.dat.
- automatic/manual registration of activation volume to orig.mgz and
overlay the activation volume on the inflated surface in tksurfer using the register.dat
I want to know if both these are valid methods and if so, what are the pros and cons of each. Seems like mri_vol2surf lets us decide what part of the volume should be projected on the surface using the projfac arguments. But the direct volume overlay in tksurfer doesn't provide that option. In that case what part of the volume is projected on to the surface?
Thanks, Zhivago...
On Sun, Jan 15, 2017 at 10:12 PM, Zhivago zhivagoa@gmail.com wrote: Thanks Bruce! Appreciate all the help,
On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 1) This is up to you. Jon Polimeni had a nice paper describing the trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface).
2) This is also up to you.Read the help in mri_vol2surf. e.g.: mri_vol2surf --help . . . --projfrac-avg min max del : average along normal 3) it is the way that we support. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hey Bruce, Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these. 1) The mri_vol2surf is used to project the activations from the GM onto an inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense? 2) When mri_vol2surf projects a volume to a surface, does it average the activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful. 3) Is mri_vol2surf the only way to view activation maps on inflated surfaces or any surface? Cheers, Zhivago... On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Zhivago 1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago... _______________________________________________ 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
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.
Thanks a lot, Bruce.
Cheers, Zhivago...
On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Zhivago
tksurfer is deprecated and uses one of the methods available in mri_vol2surf, so our advice would be to use vol2surf
cheers Bruce On Wed, 18 Jan 2017, Zhivago wrote:
[cleardot.gif]
Hi,
From whatever I read, there seem to be 2 ways for overlaying activation maps on surfaces.
- automatic/manual registration of activation volume to orig.mgz and
usage of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be overlaid on an inflated surface in freeview or tksurfer using the register.dat.
- automatic/manual registration of activation volume to orig.mgz and
overlay the activation volume on the inflated surface in tksurfer using the register.dat
I want to know if both these are valid methods and if so, what are the pros and cons of each. Seems like mri_vol2surf lets us decide what part of the volume should be projected on the surface using the projfac arguments. But the direct volume overlay in tksurfer doesn't provide that option. In that case what part of the volume is projected on to the surface?
Thanks, Zhivago...
On Sun, Jan 15, 2017 at 10:12 PM, Zhivago zhivagoa@gmail.com wrote: Thanks Bruce! Appreciate all the help,
On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 1) This is up to you. Jon Polimeni had a nice paper describing the trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface).
2) This is also up to you.Read the help in mri_vol2surf. e.g.: mri_vol2surf --help . . . --projfrac-avg min max del : average along normal 3) it is the way that we support. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hey Bruce, Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these. 1) The mri_vol2surf is used to project the activations from the GM onto an inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense? 2) When mri_vol2surf projects a volume to a surface, does it average the activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful. 3) Is mri_vol2surf the only way to view activation maps on inflated surfaces or any surface? Cheers, Zhivago... On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Zhivago 1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago... _______________________________________________ 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
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
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,
If I know the activation values at each vertex/face of a surface, can I create an mgh file independent of mri_vol2surf and overlay it on any other surface or view it independently?
Cheers, Zhivago...
On Thu, Jan 19, 2017 at 8:28 AM, Zhivago zhivagoa@gmail.com wrote:
Thanks a lot, Bruce.
Cheers, Zhivago...
On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Zhivago
tksurfer is deprecated and uses one of the methods available in mri_vol2surf, so our advice would be to use vol2surf
cheers Bruce On Wed, 18 Jan 2017, Zhivago wrote:
[cleardot.gif]
Hi,
From whatever I read, there seem to be 2 ways for overlaying activation maps on surfaces.
- automatic/manual registration of activation volume to orig.mgz and
usage of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be overlaid on an inflated surface in freeview or tksurfer using the register.dat.
- automatic/manual registration of activation volume to orig.mgz and
overlay the activation volume on the inflated surface in tksurfer using the register.dat
I want to know if both these are valid methods and if so, what are the pros and cons of each. Seems like mri_vol2surf lets us decide what part of the volume should be projected on the surface using the projfac arguments. But the direct volume overlay in tksurfer doesn't provide that option. In that case what part of the volume is projected on to the surface?
Thanks, Zhivago...
On Sun, Jan 15, 2017 at 10:12 PM, Zhivago zhivagoa@gmail.com wrote: Thanks Bruce! Appreciate all the help,
On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 1) This is up to you. Jon Polimeni had a nice paper describing the trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface).
2) This is also up to you.Read the help in mri_vol2surf. e.g.: mri_vol2surf --help . . . --projfrac-avg min max del : average along normal 3) it is the way that we support. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hey Bruce, Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these. 1) The mri_vol2surf is used to project the activations from the GM onto an inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense? 2) When mri_vol2surf projects a volume to a surface, does it average the activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful. 3) Is mri_vol2surf the only way to view activation maps on inflated surfaces or any surface? Cheers, Zhivago... On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Zhivago 1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago... _______________________________________________ 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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Yes. Easiest way it probably in matlab.
Read in a surface overlay to use as a template
overlay = MRIread('SUBJECTS_DIR/subject/surf/lh.w-g.pct.mgh');
overlay.vol = yourdata; MRIwrite('lh.yourdata.mgh')
On 01/20/2017 11:13 PM, Zhivago wrote:
Hi,
If I know the activation values at each vertex/face of a surface, can I create an mgh file independent of mri_vol2surf and overlay it on any other surface or view it independently?
Cheers, Zhivago...
On Thu, Jan 19, 2017 at 8:28 AM, Zhivago <zhivagoa@gmail.com mailto:zhivagoa@gmail.com> wrote:
Thanks a lot, Bruce. Cheers, Zhivago... On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Zhivago tksurfer is deprecated and uses one of the methods available in mri_vol2surf, so our advice would be to use vol2surf cheers Bruce On Wed, 18 Jan 2017, Zhivago wrote: [cleardot.gif] Hi, >From whatever I read, there seem to be 2 ways for overlaying activation maps on surfaces. 1) automatic/manual registration of activation volume to orig.mgz and usage of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be overlaid on an inflated surface in freeview or tksurfer using the register.dat. 2) automatic/manual registration of activation volume to orig.mgz and overlay the activation volume on the inflated surface in tksurfer using the register.dat I want to know if both these are valid methods and if so, what are the pros and cons of each. Seems like mri_vol2surf lets us decide what part of the volume should be projected on the surface using the projfac arguments. But the direct volume overlay in tksurfer doesn't provide that option. In that case what part of the volume is projected on to the surface? Thanks, Zhivago... On Sun, Jan 15, 2017 at 10:12 PM, Zhivago <zhivagoa@gmail.com <mailto:zhivagoa@gmail.com>> wrote: Thanks Bruce! Appreciate all the help, On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: 1) This is up to you. Jon Polimeni had a nice paper describing the trade-off between accurately representing the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface). 2) This is also up to you.Read the help in mri_vol2surf. e.g.: mri_vol2surf --help . . . --projfrac-avg min max del : average along normal 3) it is the way that we support. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hey Bruce, Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these. 1) The mri_vol2surf is used to project the activations from the GM onto an inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense? 2) When mri_vol2surf projects a volume to a surface, does it average the activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful. 3) Is mri_vol2surf the only way to view activation maps on inflated surfaces or any surface? Cheers, Zhivago... On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Zhivago 1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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That makes life so easy! Thanks Douglas.
Cheers, Zhivago...
On Tue, Jan 24, 2017 at 1:03 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yes. Easiest way it probably in matlab.
Read in a surface overlay to use as a template
overlay = MRIread('SUBJECTS_DIR/subject/surf/lh.w-g.pct.mgh');
overlay.vol = yourdata; MRIwrite('lh.yourdata.mgh')
On 01/20/2017 11:13 PM, Zhivago wrote:
Hi,
If I know the activation values at each vertex/face of a surface, can I create an mgh file independent of mri_vol2surf and overlay it on any other surface or view it independently?
Cheers, Zhivago...
On Thu, Jan 19, 2017 at 8:28 AM, Zhivago <zhivagoa@gmail.com mailto:zhivagoa@gmail.com> wrote:
Thanks a lot, Bruce. Cheers, Zhivago... On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Zhivago tksurfer is deprecated and uses one of the methods available in mri_vol2surf, so our advice would be to use vol2surf cheers Bruce On Wed, 18 Jan 2017, Zhivago wrote: [cleardot.gif] Hi, >From whatever I read, there seem to be 2 ways for overlaying activation maps on surfaces. 1) automatic/manual registration of activation volume to orig.mgz and usage of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be overlaid on an inflated surface in freeview or tksurfer using the register.dat. 2) automatic/manual registration of activation volume to orig.mgz and overlay the activation volume on the inflated surface in tksurfer using the register.dat I want to know if both these are valid methods and if so, what are the pros and cons of each. Seems like mri_vol2surf lets us decide what part of the volume should be projected on the surface using the projfac arguments. But the direct volume overlay in tksurfer doesn't provide that option. In that case what part of the volume is projected on to the surface? Thanks, Zhivago... On Sun, Jan 15, 2017 at 10:12 PM, Zhivago <zhivagoa@gmail.com <mailto:zhivagoa@gmail.com>> wrote: Thanks Bruce! Appreciate all the help, On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: 1) This is up to you. Jon Polimeni had a nice paper describing the trade-off between accuratelyrepresenting
the local neural response (which is best at the white border) and statistical power (which is best nearer the pial surface). 2) This is also up to you.Read the help inmri_vol2surf.
e.g.: mri_vol2surf --help . . . --projfrac-avg min max del : average along normal 3) it is the way that we support. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hey Bruce, Thank you very much for the responses! Had posted a couple of more questions, but looks like it hasn't gone across. Will really appreciate it if you can provide some answers to these. 1) The mri_vol2surf is used to project the activations from the GM onto an inflated surface, which is usually the inflated smoothwm surface output from reconall. Will it be more accurate to use the inflated version of the intermediate surface, like halfway between the white and pial matter? Will it make any kind of sense? 2) When mri_vol2surf projects a volume to a surface, does it average the activation values of voxels along the cortical depth or sum it? What really happens beneath? Any amount of insight will be helpful. 3) Is mri_vol2surf the only way to view activation maps on inflated surfaces or any surface? Cheers, Zhivago... On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Zhivago 1) You can project from inside the ?h.white surface if projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it starts to get arbitrary. 2) The default projfrac, as documented in the -help response, is 0. 3) Yes, 0-->white matter boundary. 1--> pial boundary. 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, which is a scalar field over the surface. cheers Bruce On Sun, 15 Jan 2017, Zhivago wrote: Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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to whom it is addressed. If you believe this e-mail was sent to you inerror
and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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