External Email - Use Caution
Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer.
I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation:
1 - Create a register.dat by using fsl identity matrix since I am already in the native space: tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat> 2 - Then, using this register.dat to make surfaces from the 4D timeseries with: mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz> I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this.
Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ?
Best, Ozzy
On 5/11/2020 5:53 PM, özenç taskin wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer.
I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation:
1 - Create a register.dat by using fsl identity matrix since I am already in the native space:
tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat>
This is ok, but unnecessary. You can use --regheader subject in mri_vol2surf below instead of --reg
2 - Then, using this register.dat to make surfaces from the 4D timeseries with:
mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz>
Add --projfrac 0.5 to sample in the middle of the ribbon.
I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this.
Time series are no different than a single frame. You can actually map directly to fsaverage in mri_vol2surf with --trgsubject fsaverage (or you can take the vol2surf output and run mri_surf2surf on it)
Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ?
No, you do not. That page just talks about if you want an actual surface file with xyz in the native coordinates. You do not need to have this file.
Best, Ozzy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz with tkregister2 instead of rawavg.mgz if the aim is to get surface maps in native space, am I right ? And by native space I mean the subjects' native brain structure and not necessarily the native xyz coordinates (I guess conformed space is the right term for this, but I am not sure).
Best, Ozzy
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, May 13, 2020 3:07 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume timeseries to native and fsaverage
On 5/11/2020 5:53 PM, özenç taskin wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer.
I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation:
1 - Create a register.dat by using fsl identity matrix since I am already in the native space: tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat> This is ok, but unnecessary. You can use --regheader subject in mri_vol2surf below instead of --reg 2 - Then, using this register.dat to make surfaces from the 4D timeseries with: mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz> Add --projfrac 0.5 to sample in the middle of the ribbon. I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this. Time series are no different than a single frame. You can actually map directly to fsaverage in mri_vol2surf with --trgsubject fsaverage (or you can take the vol2surf output and run mri_surf2surf on it)
Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ? No, you do not. That page just talks about if you want an actual surface file with xyz in the native coordinates. You do not need to have this file.
Best, Ozzy
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
oh, if you want them in conformed space, they are already there
On 5/18/2020 11:34 AM, özenç taşkın wrote:
External Email - Use Caution
Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz with tkregister2 instead of rawavg.mgz if the aim is to get surface maps in native space, am I right ? And by native space I mean the subjects' native brain structure and not necessarily the native xyz coordinates (I guess conformed space is the right term for this, but I am not sure).
Best, Ozzy
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, May 13, 2020 3:07 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Volume timeseries to native and fsaverage
On 5/11/2020 5:53 PM, özenç taskin wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer.
I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation:
1 - Create a register.dat by using fsl identity matrix since I am already in the native space:
tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat>This is ok, but unnecessary. You can use --regheader subject in mri_vol2surf below instead of --reg
2 - Then, using this register.dat to make surfaces from the 4D timeseries with:
mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz>Add --projfrac 0.5 to sample in the middle of the ribbon.
I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this.
Time series are no different than a single frame. You can actually map directly to fsaverage in mri_vol2surf with --trgsubject fsaverage (or you can take the vol2surf output and run mri_surf2surf on it)
Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ?
No, you do not. That page just talks about if you want an actual surface file with xyz in the native coordinates. You do not need to have this file.
Best, Ozzy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
External Email - Use Caution
Hi Doug,
I think I might have some gaps in my knowledge regarding the type of surface spaces Freesurfer uses and can produce, so I wanted to make sure that I got everything right. So my belief is that Freesurfer has the conformed surfaces which represent subjects' native topography, but they are built from the isotropic version of the images (orig.mgz) and these are actually the default outputs of Freesurfer. Then, we can produce the native space surfaces in the native T1 resolution which follows the original xyz coordinates by following the commands mentioned on the FSAnat to NativeAnat page using the rawavg.mgz. Finally, we have the standard template spaces such as fsaverage which the spheres that are created from the conformed surfaces are registered to.
One thing I forgot to mention about the data I have is that my EPI images are in the same space with my T1 images, but they keep their original resolution. Do I need to resample them in order to map them to any of these surface spaces ? If that is the case, I believe depending on the surface space I want to end up with I also should use different target images for this resampling. For instance, if I want to create maps in the conformed surfaces, I need to resample them to the resolution of my orig.mgz and for the native surfaces, I should use the rawavg.mgz. Am I right about all these ? If so, I think I now know how to approach this a little bit better.
Best, Ozzy
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, May 18, 2020 8:37 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume timeseries to native and fsaverage
oh, if you want them in conformed space, they are already there
On 5/18/2020 11:34 AM, özenç taşkın wrote:
External Email - Use Caution
Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz with tkregister2 instead of rawavg.mgz if the aim is to get surface maps in native space, am I right ? And by native space I mean the subjects' native brain structure and not necessarily the native xyz coordinates (I guess conformed space is the right term for this, but I am not sure).
Best, Ozzy
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, May 13, 2020 3:07 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume timeseries to native and fsaverage
On 5/11/2020 5:53 PM, özenç taskin wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer.
I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation:
1 - Create a register.dat by using fsl identity matrix since I am already in the native space: tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat> This is ok, but unnecessary. You can use --regheader subject in mri_vol2surf below instead of --reg 2 - Then, using this register.dat to make surfaces from the 4D timeseries with: mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz> Add --projfrac 0.5 to sample in the middle of the ribbon. I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this. Time series are no different than a single frame. You can actually map directly to fsaverage in mri_vol2surf with --trgsubject fsaverage (or you can take the vol2surf output and run mri_surf2surf on it)
Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ? No, you do not. That page just talks about if you want an actual surface file with xyz in the native coordinates. You do not need to have this file.
Best, Ozzy
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm still confused as to what you are trying to do. If you just want to sample your data onto the surface, then you do not need to resample it at all. You just run mri_vol2surf with the appropriate registration and projection fraction. If I'm misunderstanding, please clarify.
On 5/19/2020 4:27 PM, özenç taşkın wrote:
External Email - Use Caution
Hi Doug,
I think I might have some gaps in my knowledge regarding the type of surface spaces Freesurfer uses and can produce, so I wanted to make sure that I got everything right. So my belief is that Freesurfer has the conformed surfaces which represent subjects' native topography, but they are built from the isotropic version of the images (orig.mgz) and these are actually the default outputs of Freesurfer. Then, we can produce the native space surfaces in the native T1 resolution which follows the original xyz coordinates by following the commands mentioned on the FSAnat to NativeAnat page using the rawavg.mgz. Finally, we have the standard template spaces such as fsaverage which the spheres that are created from the conformed surfaces are registered to.
One thing I forgot to mention about the data I have is that my EPI images are in the same space with my T1 images, but they keep their original resolution. Do I need to resample them in order to map them to any of these surface spaces ? If that is the case, I believe depending on the surface space I want to end up with I also should use different target images for this resampling. For instance, if I want to create maps in the conformed surfaces, I need to resample them to the resolution of my orig.mgz and for the native surfaces, I should use the rawavg.mgz. Am I right about all these ? If so, I think I now know how to approach this a little bit better.
Best, Ozzy
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, May 18, 2020 8:37 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Volume timeseries to native and fsaverage oh, if you want them in conformed space, they are already there
On 5/18/2020 11:34 AM, özenç taşkın wrote:
External Email - Use Caution
Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz with tkregister2 instead of rawavg.mgz if the aim is to get surface maps in native space, am I right ? And by native space I mean the subjects' native brain structure and not necessarily the native xyz coordinates (I guess conformed space is the right term for this, but I am not sure).
Best, Ozzy
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Wednesday, May 13, 2020 3:07 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Volume timeseries to native and fsaverage
On 5/11/2020 5:53 PM, özenç taskin wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer.
I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation:
1 - Create a register.dat by using fsl identity matrix since I am already in the native space:
tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat>This is ok, but unnecessary. You can use --regheader subject in mri_vol2surf below instead of --reg
2 - Then, using this register.dat to make surfaces from the 4D timeseries with:
mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz>Add --projfrac 0.5 to sample in the middle of the ribbon.
I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this.
Time series are no different than a single frame. You can actually map directly to fsaverage in mri_vol2surf with --trgsubject fsaverage (or you can take the vol2surf output and run mri_surf2surf on it)
Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ?
No, you do not. That page just talks about if you want an actual surface file with xyz in the native coordinates. You do not need to have this file.
Best, Ozzy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
-
Douglas N. Greve -
özenç taskin -
özenç taşkın