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Hello all,
I have a series of functionally-defined ROI volumes (.nii format) that I'd like to project into the white matter to then be used for tractography.
So far the vols have been brought from cvs_avg35 space into subject space from using mri_vol2vol and the corresponding m3z file. This was followed by mri_vol2vol using the registration from bbregister to get the functional regions into diffusion space.
I have done this for the ROIs in their original GM volume, but would now like to also have corresponding WM volumes for tractography.
What is the best way to go about doing this?
Thanks,
Corinna
Hi Corinna, if I understand correctly, you basically have cortical GM ROIs in CVS space and you want to create an ROI of the adjacent WM. Is that right? How far do you want to extend the ROI into WM? Do you want to do something like a wmparc.mgz? doug
On 12/18/19 9:55 AM, Corinna Bauer wrote:
External Email - Use Caution
Hello all,
I have a series of functionally-defined ROI volumes (.nii format) that I'd like to project into the white matter to then be used for tractography.
So far the vols have been brought from cvs_avg35 space into subject space from using mri_vol2vol and the corresponding m3z file. This was followed by mri_vol2vol using the registration from bbregister to get the functional regions into diffusion space.
I have done this for the ROIs in their original GM volume, but would now like to also have corresponding WM volumes for tractography.
What is the best way to go about doing this?
Thanks,
Corinna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug, Yes, I have GM ROIs in CVS space and I'd like to create a corresponding WM ROI for each of them that extends 2-3 voxels into the WM. Would it be possible to create something akin to wmparc.mgz with these ROIs?
Corinna
On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Hi Corinna, if I understand correctly, you basically have cortical GM ROIs in CVS space and you want to create an ROI of the adjacent WM. Is that right? How far do you want to extend the ROI into WM? Do you want to do something like a wmparc.mgz? doug
On 12/18/19 9:55 AM, Corinna Bauer wrote:
External Email - Use CautionHello all,
I have a series of functionally-defined ROI volumes (.nii format) that I'd like to project into the white matter to then be used for tractography.
So far the vols have been brought from cvs_avg35 space into subject space from using mri_vol2vol and the corresponding m3z file. This was followed by mri_vol2vol using the registration from bbregister to get the functional regions into diffusion space.
I have done this for the ROIs in their original GM volume, but would now like to also have corresponding WM volumes for tractography.
What is the best way to go about doing this?
Thanks,
Corinna
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off the top of my head I can think of a couple of ways 1. replicate the wmparc.mgz stream. For this you will need to create an annotation from your GM ROIs by combining them into a ssegmenation, then using mri_vol2surf to create a surface-based segmentation, then using mris_seg2annot, then use mri_aparc2aseg to create an aparc+aseg.mgz type file, then mri_aparc2aseg again to create the wmparc.mgz type file. This will take some trial an error as the command lines are a bit picky (esp mris_seg2annot) 2. simple dilation of the GM ROIs followed by taking an intersection with the WM mask. You can use mri_binarize to create the WM mask, then, for each GM ROI, use mri_binarize with the --dilate option to dilate a few voxels, then something like fscalc wmmask.mgz and roidilated.mgz -o roidilated-in-wm.mgz
On 12/18/19 2:33 PM, Corinna Bauer wrote:
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Hi Doug, Yes, I have GM ROIs in CVS space and I'd like to create a corresponding WM ROI for each of them that extends 2-3 voxels into the WM. Would it be possible to create something akin to wmparc.mgz with these ROIs?
Corinna
On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Hi Corinna, if I understand correctly, you basically have cortical GM ROIs in CVS space and you want to create an ROI of the adjacent WM. Is that right? How far do you want to extend the ROI into WM? Do you want to do something like a wmparc.mgz? doug On 12/18/19 9:55 AM, Corinna Bauer wrote: > > External Email - Use Caution > > Hello all, > > I have a series of functionally-defined ROI volumes (.nii format) that > I'd like to project into the white matter to then be used for > tractography. > > So far the vols have been brought from cvs_avg35 space into subject > space from using mri_vol2vol and the corresponding m3z file. This was > followed by mri_vol2vol using the registration from bbregister to get > the functional regions into diffusion space. > > I have done this for the ROIs in their original GM volume, but would > now like to also have corresponding WM volumes for tractography. > > What is the best way to go about doing this? > > Thanks, > > Corinna > > > > _______________________________________________ > 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
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Ok thanks! The first option sounds like it might provide a cleaner result, since the second would dilate in all dimensions. I'll let you know if I run into any trouble with it.
Thanks again,
Corinna
On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
off the top of my head I can think of a couple of ways
- replicate the wmparc.mgz stream. For this you will need to create an
annotation from your GM ROIs by combining them into a ssegmenation, then using mri_vol2surf to create a surface-based segmentation, then using mris_seg2annot, then use mri_aparc2aseg to create an aparc+aseg.mgz type file, then mri_aparc2aseg again to create the wmparc.mgz type file. This will take some trial an error as the command lines are a bit picky (esp mris_seg2annot) 2. simple dilation of the GM ROIs followed by taking an intersection with the WM mask. You can use mri_binarize to create the WM mask, then, for each GM ROI, use mri_binarize with the --dilate option to dilate a few voxels, then something like fscalc wmmask.mgz and roidilated.mgz -o roidilated-in-wm.mgz
On 12/18/19 2:33 PM, Corinna Bauer wrote:
External Email - Use CautionHi Doug, Yes, I have GM ROIs in CVS space and I'd like to create a corresponding WM ROI for each of them that extends 2-3 voxels into the
WM.
Would it be possible to create something akin to wmparc.mgz with these ROIs?
Corinna
On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Hi Corinna, if I understand correctly, you basically have cortical GM ROIs in CVS space and you want to create an ROI of the adjacent WM. Is that right? How far do you want to extend the ROI into WM? Do you want to do something like a wmparc.mgz? doug On 12/18/19 9:55 AM, Corinna Bauer wrote: > > External Email - Use Caution > > Hello all, > > I have a series of functionally-defined ROI volumes (.nii format) that > I'd like to project into the white matter to then be used for > tractography. > > So far the vols have been brought from cvs_avg35 space into subject > space from using mri_vol2vol and the corresponding m3z file. This was > followed by mri_vol2vol using the registration from bbregister to get > the functional regions into diffusion space. > > I have done this for the ROIs in their original GM volume, but would > now like to also have corresponding WM volumes for tractography. > > What is the best way to go about doing this? > > Thanks, > > Corinna > > > > _______________________________________________ > 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
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Yes. The 2nd would dilate in all dimensions, but you would only keep those voxels that were in WM. but the 1st is definitely cleaner
On 12/18/19 2:52 PM, Corinna Bauer wrote:
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Ok thanks! The first option sounds like it might provide a cleaner result, since the second would dilate in all dimensions. I'll let you know if I run into any trouble with it.
Thanks again,
Corinna
On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
off the top of my head I can think of a couple of ways 1. replicate the wmparc.mgz stream. For this you will need to create an annotation from your GM ROIs by combining them into a ssegmenation, then using mri_vol2surf to create a surface-based segmentation, then using mris_seg2annot, then use mri_aparc2aseg to create an aparc+aseg.mgz type file, then mri_aparc2aseg again to create the wmparc.mgz type file. This will take some trial an error as the command lines are a bit picky (esp mris_seg2annot) 2. simple dilation of the GM ROIs followed by taking an intersection with the WM mask. You can use mri_binarize to create the WM mask, then, for each GM ROI, use mri_binarize with the --dilate option to dilate a few voxels, then something like fscalc wmmask.mgz and roidilated.mgz -o roidilated-in-wm.mgz On 12/18/19 2:33 PM, Corinna Bauer wrote: > > External Email - Use Caution > > Hi Doug, > Yes, I have GM ROIs in CVS space and I'd like to create a > corresponding WM ROI for each of them that extends 2-3 voxels into the WM. > Would it be possible to create something akin to wmparc.mgz with these > ROIs? > > Corinna > > On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Hi Corinna, if I understand correctly, you basically have cortical GM > ROIs in CVS space and you want to create an ROI of the adjacent > WM. Is > that right? How far do you want to extend the ROI into WM? Do you > want > to do something like a wmparc.mgz? > doug > > On 12/18/19 9:55 AM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Hello all, > > > > I have a series of functionally-defined ROI volumes (.nii > format) that > > I'd like to project into the white matter to then be used for > > tractography. > > > > So far the vols have been brought from cvs_avg35 space into subject > > space from using mri_vol2vol and the corresponding m3z file. > This was > > followed by mri_vol2vol using the registration from bbregister > to get > > the functional regions into diffusion space. > > > > I have done this for the ROIs in their original GM volume, but > would > > now like to also have corresponding WM volumes for tractography. > > > > What is the best way to go about doing this? > > > > Thanks, > > > > Corinna > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Would it be best to do option 1 in the CVS space or in subject space?
On Wed, Dec 18, 2019 at 2:57 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Yes. The 2nd would dilate in all dimensions, but you would only keep those voxels that were in WM. but the 1st is definitely cleaner
On 12/18/19 2:52 PM, Corinna Bauer wrote:
External Email - Use CautionOk thanks! The first option sounds like it might provide a cleaner result, since the second would dilate in all dimensions. I'll let you know if I run into any trouble with it.
Thanks again,
Corinna
On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
off the top of my head I can think of a couple of ways 1. replicate the wmparc.mgz stream. For this you will need to create an annotation from your GM ROIs by combining them into a ssegmenation, then using mri_vol2surf to create a surface-based segmentation, then using mris_seg2annot, then use mri_aparc2aseg to create an aparc+aseg.mgz type file, then mri_aparc2aseg again to create the wmparc.mgz type file. This will take some trial an error as the command lines are a bit picky (esp mris_seg2annot) 2. simple dilation of the GM ROIs followed by taking an intersection with the WM mask. You can use mri_binarize to create the WM mask, then, for each GM ROI, use mri_binarize with the --dilate option to dilate a few voxels, then something like fscalc wmmask.mgz and roidilated.mgz -o roidilated-in-wm.mgz On 12/18/19 2:33 PM, Corinna Bauer wrote: > > External Email - Use Caution > > Hi Doug, > Yes, I have GM ROIs in CVS space and I'd like to create a > corresponding WM ROI for each of them that extends 2-3 voxels into the WM. > Would it be possible to create something akin to wmparc.mgz with these > ROIs? > > Corinna > > On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Hi Corinna, if I understand correctly, you basically have cortical GM > ROIs in CVS space and you want to create an ROI of the adjacent > WM. Is > that right? How far do you want to extend the ROI into WM? Do you > want > to do something like a wmparc.mgz? > doug > > On 12/18/19 9:55 AM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Hello all, > > > > I have a series of functionally-defined ROI volumes (.nii > format) that > > I'd like to project into the white matter to then be used for > > tractography. > > > > So far the vols have been brought from cvs_avg35 space into subject > > space from using mri_vol2vol and the corresponding m3z file. > This was > > followed by mri_vol2vol using the registration frombbregister
> to get > > the functional regions into diffusion space. > > > > I have done this for the ROIs in their original GM volume,but
> would > > now like to also have corresponding WM volumes for tractography. > > > > What is the best way to go about doing this? > > > > Thanks, > > > > Corinna > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
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yes, either should work.
On 12/18/19 3:15 PM, Corinna Bauer wrote:
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Would it be best to do option 1 in the CVS space or in subject space?
On Wed, Dec 18, 2019 at 2:57 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Yes. The 2nd would dilate in all dimensions, but you would only keep those voxels that were in WM. but the 1st is definitely cleaner On 12/18/19 2:52 PM, Corinna Bauer wrote: > > External Email - Use Caution > > Ok thanks! The first option sounds like it might provide a cleaner > result, since the second would dilate in all dimensions. > I'll let you know if I run into any trouble with it. > > Thanks again, > > Corinna > > > On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > off the top of my head I can think of a couple of ways > 1. replicate the wmparc.mgz stream. For this you will need to > create an > annotation from your GM ROIs by combining them into a > ssegmenation, then > using mri_vol2surf to create a surface-based segmentation, then using > mris_seg2annot, then use mri_aparc2aseg to create an > aparc+aseg.mgz type > file, then mri_aparc2aseg again to create the wmparc.mgz type > file. This > will take some trial an error as the command lines are a bit picky > (esp > mris_seg2annot) > 2. simple dilation of the GM ROIs followed by taking an intersection > with the WM mask. You can use mri_binarize to create the WM mask, > then, > for each GM ROI, use mri_binarize with the --dilate option to > dilate a > few voxels, then something like fscalc wmmask.mgz and > roidilated.mgz -o > roidilated-in-wm.mgz > > > On 12/18/19 2:33 PM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Hi Doug, > > Yes, I have GM ROIs in CVS space and I'd like to create a > > corresponding WM ROI for each of them that extends 2-3 voxels > into the WM. > > Would it be possible to create something akin to wmparc.mgz with > these > > ROIs? > > > > Corinna > > > > On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > Hi Corinna, if I understand correctly, you basically have > cortical GM > > ROIs in CVS space and you want to create an ROI of the adjacent > > WM. Is > > that right? How far do you want to extend the ROI into WM? > Do you > > want > > to do something like a wmparc.mgz? > > doug > > > > On 12/18/19 9:55 AM, Corinna Bauer wrote: > > > > > > External Email - Use Caution > > > > > > Hello all, > > > > > > I have a series of functionally-defined ROI volumes (.nii > > format) that > > > I'd like to project into the white matter to then be used for > > > tractography. > > > > > > So far the vols have been brought from cvs_avg35 space > into subject > > > space from using mri_vol2vol and the corresponding m3z file. > > This was > > > followed by mri_vol2vol using the registration from bbregister > > to get > > > the functional regions into diffusion space. > > > > > > I have done this for the ROIs in their original GM volume, but > > would > > > now like to also have corresponding WM volumes for > tractography. > > > > > > What is the best way to go about doing this? > > > > > > Thanks, > > > > > > Corinna > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto: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> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Greve, Douglas N.,Ph.D.