Thank you Bruce... This is very helpful!
Bests,
John
John
Sent: Wednesday, June 08, 2016 at 9:32 AM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Break 3D volume
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Break 3D volume
the help is old! <src dir> should be <src volume>. (x0,y0,z0) is the
starting point of your bounding box, and (dx,dy,dz) is the extent of it (in
voxels)
On Wed, 8 Jun 2016, John
Anderson wrote:
> Hi Bruce,
> Thank you for the quick response. it is really highly appreciated!
> I have 3D mask in the form of nifti file and it has the shape of large
> square( the black big square in my figure). I wanted to divid it to a
> smaller and equale volumes. It iseems that mri_extract can support my
> objectives:
> Please how can I use this command. I was unable to find any instructions:
> If my 3D maks is "mask.nii" and the command is mri_extract <src_dir> x0 y0
> z0 dx dy dz <dst_dir> how can I use the command properly?
> <src_dir>: is this where my file is located?
> x0 y0 z0 dx dy dz: What I should use here?
>
> Thank you very much for your help
>
>
> John
> Sent: Wednesday, June 08, 2016 at 9:13 AM
> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Break 3D volume
> Hi John
>
> I'm not exactly sure what you mean, but you can use mri_extract to pull
> out rectangular subvolumes.
>
> cheers
> Bruce
> On Wed, 8 Jun 2016, John Anderson wrote:
>
> > Dear FS Experts,
> > Are there any tools in Freesurfer or Matlab scripts that can help to break
> > down a 3D volume ( created using mri_volsynth) to a multiple equal sub
> > volumes ( like the attached figure )
> > Thanks in a dvance for any suggestion!
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> >
> >
> >
> > [IMAGE]
> >
> >_______________________________________________
> 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
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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
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starting point of your bounding box, and (dx,dy,dz) is the extent of it (in
voxels)
On Wed, 8 Jun 2016, John
Anderson wrote:
> Hi Bruce,
> Thank you for the quick response. it is really highly appreciated!
> I have 3D mask in the form of nifti file and it has the shape of large
> square( the black big square in my figure). I wanted to divid it to a
> smaller and equale volumes. It iseems that mri_extract can support my
> objectives:
> Please how can I use this command. I was unable to find any instructions:
> If my 3D maks is "mask.nii" and the command is mri_extract <src_dir> x0 y0
> z0 dx dy dz <dst_dir> how can I use the command properly?
> <src_dir>: is this where my file is located?
> x0 y0 z0 dx dy dz: What I should use here?
>
> Thank you very much for your help
>
>
> John
> Sent: Wednesday, June 08, 2016 at 9:13 AM
> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Break 3D volume
> Hi John
>
> I'm not exactly sure what you mean, but you can use mri_extract to pull
> out rectangular subvolumes.
>
> cheers
> Bruce
> On Wed, 8 Jun 2016, John Anderson wrote:
>
> > Dear FS Experts,
> > Are there any tools in Freesurfer or Matlab scripts that can help to break
> > down a 3D volume ( created using mri_volsynth) to a multiple equal sub
> > volumes ( like the attached figure )
> > Thanks in a dvance for any suggestion!
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> >
> >
> >
> > [IMAGE]
> >
> >_______________________________________________
> 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
> 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.
