Hi again I need the volume corresponding exactly to the ?h.white because I am doing some tractography and my ROI are coming from the parcellation, so the tractography mask should be the same than ?h.white. that's why I can not use the aseg. MRI-fill is more or less the same than imfill in matlab, isn't it? I was looking for something that fill the volume from the mesh for mere accuracy..

Leila

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: mercredi, 15. août 2007 22:03 To: Doug Greve Cc: freesurfer@nmr.mgh.harvard.edu; Leila BH Subject: Re: [Freesurfer] mri_surf2vol

or use mris_fill On Wed, 15 Aug 2007, Doug Greve wrote:

Do you want everything in the white surface? That would include more than

WM.

If you want just WM, you can use the aseg.mgz, something like:

mri_binarize --i aseg.mgz --match 2 --match 41 --o wm.only.mgz

you may need a new copy of mri_binarize ...

Leila BH wrote:

...

Hello,

I need to convert the white matte surface to a volume :binary volume with

1

...

in white matter and 0 outside. I am using the mri_surf2vol command (on both hemisphere), and fill it using matlab. Do you know if it is possible

...

to obtain the volume from the surface already filled ?

Thanks a lot.

Here is the command I use :

Mri_surf2vol --mkmask --hemi lh --template /my_image.img --volregidentity

...

mysubject --outvol outputvol_lh.img

---

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I need everything inside the ribbon,

I can see in the web the fuction mris_volmask that could help me, but I don’t find in my freesurfer (version :stable3)??

An alternative solution I found is the mri_aprac2aseg (with - - ribbon), and tka only tha voxel with value smaller than 1000. it seems like the volume (filled) of the ?h.white.

Is is true? Or the is better solution?

Thanks

Ps: an other small but stupid question: to convert this mask to analyze I use mri_convert but I don’t find a way to have my input in 128*128*128 (and not 256 *256 *256), with mri_label2vol I used –temp but that doesn’t work with mri_convert

_____

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: mercredi, 15. août 2007 23:11 To: Leila BH Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2vol

Do you want a mask of just the ribbon or everything inside the ribbon or only white matter inside the ribbon?

Leila BH wrote:

Hi again I need the volume corresponding exactly to the ?h.white because I am doing some tractography and my ROI are coming from the parcellation, so the tractography mask should be the same than ?h.white. that's why I can not use the aseg. MRI-fill is more or less the same than imfill in matlab, isn't it? I was looking for something that fill the volume from the mesh for mere accuracy..

Leila

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: mercredi, 15. août 2007 22:03 To: Doug Greve Cc: freesurfer@nmr.mgh.harvard.edu; Leila BH Subject: Re: [Freesurfer] mri_surf2vol

or use mris_fill On Wed, 15 Aug 2007, Doug Greve wrote:

Do you want everything in the white surface? That would include more than

WM.

If you want just WM, you can use the aseg.mgz, something like:

mri_binarize --i aseg.mgz --match 2 --match 41 --o wm.only.mgz

you may need a new copy of mri_binarize ...

Leila BH wrote:

Hello,

I need to convert the white matte surface to a volume :binary volume with

1

in white matter and 0 outside. I am using the mri_surf2vol command (on both hemisphere), and fill it using matlab. Do you know if it is possible

to obtain the volume from the surface already filled ?

Thanks a lot.

Here is the command I use :

Mri_surf2vol --mkmask --hemi lh --template /my_image.img --volregidentity

mysubject --outvol outputvol_lh.img

------------------------------------------------------------------------

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer