Dear Fs Experts, What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum)
Thanks Mohamad
Hi Mohamad
the wm.seg.mgz is the output of mri_segment and is a voxel segmentation that considers local intensities and estimated cortical geometry, but not topology. mri_pretess then takes the wm.seg.mgz and removes certain pathological voxel configurations (like corners touching) that mess up the subsequent tessellation and creates the wm.mgz
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum)
Thanks
Mohamad
Thank you Bruce, Then what is the white area means in (wm.mgz); kindly check the attached photo ALSO do you recommend to use wm.mgz and wm.seg.mgz in order to create a mask for the white matter.
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 1:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
Hi Mohamad
the wm.seg.mgz is the output of mri_segment and is a voxel segmentation that considers local intensities and estimated cortical geometry, but not topology. mri_pretess then takes the wm.seg.mgz and removes certain pathological voxel configurations (like corners touching) that mess up the subsequent tessellation and creates the wm.mgz
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum)
Thanks
Mohamad
the white is a region on the midline, probably ventricle, that we fill to create a closed surface for the cortical models. If you want a white matter mask you are better off extracting it from the aseg.mgz with mri_binarize -match
cheers Bruce On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Thank you Bruce, Then what is the white area means in (wm.mgz); kindly check the attached photo ALSO do you recommend to use wm.mgz and wm.seg.mgz in order to create a mask for the white matter.
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 1:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
Hi Mohamad
the wm.seg.mgz is the output of mri_segment and is a voxel segmentation that considers local intensities and estimated cortical geometry, but not topology. mri_pretess then takes the wm.seg.mgz and removes certain pathological voxel configurations (like corners touching) that mess up the subsequent tessellation and creates the wm.mgz
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum)
Thanks
Mohamad
Thanks, Actually I tried to create a mask for the cerebellum using mri_binarize --i aseg.mgz --o cerebellum.mgz --match 7 46 . Then I re positioned this mask in the same direction of the standard template MNI152 using fslreorient2std <input> <output>. Finally I registered this mask linearely using FLIRT GUI in FSL (Translational only 3 parameter model) to FA map. When I used fslview to view the results there was no overlap between the mask and the FA map. That's why I am looking for a new way to create my a mask.
Kindly check the attached photo and thanks SO VERY MUCH for your help Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 2:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
the white is a region on the midline, probably ventricle, that we fill to create a closed surface for the cortical models. If you want a white matter mask you are better off extracting it from the aseg.mgz with mri_binarize -match
cheers Bruce On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Thank you Bruce, Then what is the white area means in (wm.mgz); kindly check the attached photo ALSO do you recommend to use wm.mgz and wm.seg.mgz in order to create a mask for the white matter.
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 1:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
Hi Mohamad
the wm.seg.mgz is the output of mri_segment and is a voxel segmentation that considers local intensities and estimated cortical geometry, but not topology. mri_pretess then takes the wm.seg.mgz and removes certain pathological voxel configurations (like corners touching) that mess up the subsequent tessellation and creates the wm.mgz
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum)
Thanks
Mohamad
that sounds like a problem with the registration/transformation not the mask itself. Why are you doing only translation? There will certainly be a rotation. Have you tried using bbregister for this? It's what we use, and in general works really well (so well that the MJ ported it to FSL!)
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Thanks, Actually I tried to create a mask for the cerebellum using mri_binarize --i aseg.mgz --o cerebellum.mgz --match 7 46 . Then I re positioned this mask in the same direction of the standard template MNI152 using fslreorient2std <input> <output>. Finally I registered this mask linearely using FLIRT GUI in FSL (Translational only 3 parameter model) to FA map. When I used fslview to view the results there was no overlap between the mask and the FA map. That's why I am looking for a new way to create my a mask.
Kindly check the attached photo and thanks SO VERY MUCH for your help Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 2:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
the white is a region on the midline, probably ventricle, that we fill to create a closed surface for the cortical models. If you want a white matter mask you are better off extracting it from the aseg.mgz with mri_binarize -match
cheers Bruce On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Thank you Bruce, Then what is the white area means in (wm.mgz); kindly check the attached photo ALSO do you recommend to use wm.mgz and wm.seg.mgz in order to create a mask for the white matter.
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 1:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
Hi Mohamad
the wm.seg.mgz is the output of mri_segment and is a voxel segmentation that considers local intensities and estimated cortical geometry, but not topology. mri_pretess then takes the wm.seg.mgz and removes certain pathological voxel configurations (like corners touching) that mess up the subsequent tessellation and creates the wm.mgz
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum)
Thanks
Mohamad
Hi Bruce, bbregister worked very well :)
Thank you
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 2:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] FW: The difference between wm.mgz and wm.seg.mgz
that sounds like a problem with the registration/transformation not the mask itself. Why are you doing only translation? There will certainly be a rotation. Have you tried using bbregister for this? It's what we use, and in general works really well (so well that the MJ ported it to FSL!)
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Thanks, Actually I tried to create a mask for the cerebellum using mri_binarize --i aseg.mgz --o cerebellum.mgz --match 7 46 . Then I re positioned this mask in the same direction of the standard template MNI152 using fslreorient2std <input> <output>. Finally I registered this mask linearely using FLIRT GUI in FSL (Translational only 3 parameter model) to FA map. When I used fslview to view the results there was no overlap between the mask and the FA map. That's why I am looking for a new way to create my a mask.
Kindly check the attached photo and thanks SO VERY MUCH for your help Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 2:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
the white is a region on the midline, probably ventricle, that we fill to create a closed surface for the cortical models. If you want a white matter mask you are better off extracting it from the aseg.mgz with mri_binarize -match
cheers Bruce On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Thank you Bruce, Then what is the white area means in (wm.mgz); kindly check the attached photo ALSO do you recommend to use wm.mgz and wm.seg.mgz in order to create a mask for the white matter.
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 1:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz
Hi Mohamad
the wm.seg.mgz is the output of mri_segment and is a voxel segmentation that considers local intensities and estimated cortical geometry, but not topology. mri_pretess then takes the wm.seg.mgz and removes certain pathological voxel configurations (like corners touching) that mess up the subsequent tessellation and creates the wm.mgz
cheers Bruce
On Tue, 29 Jul 2014, Alshikho, Mohamad J. wrote:
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum)
Thanks
Mohamad
freesurfer@nmr.mgh.harvard.edu
-
Alshikho, Mohamad J. -
Bruce Fischl