[Freesurfer] How to convert a surface to volume space after using mris_preproc?

2012-04-19 Thread Long 
Hi all,

I had a question when convert a surface to volume space.

First, I converted a volume nifti data to fsaverage:

mris_preproc --target fsaverage --hemi lh --iv data.nii bb_register.dat
--out data.lh.mgh

Then, I want to convert the data.lh.mgh to volume space, I tried
mri_surf2vol, however, it needs register.dat. As I understood, the
data.lh.mgh was already registered to fsaverage surface, so how can I get
the required register.dat file? Thank you for your attention.

Best,
Xiangyu
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Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?

2012-04-23 Thread Douglas N Greve 
Hi Xiangyu, just add  --identity fsaverage  to the surf2vol command line
doug


On 04/19/2012 05:57 PM, Long wrote:
> Hi all,
>
> I had a question when convert a surface to volume space.
>
> First, I converted a volume nifti data to fsaverage:
>
> mris_preproc --target fsaverage --hemi lh --iv data.nii 
> bb_register.dat --out data.lh.mgh
>
> Then, I want to convert the data.lh.mgh to volume space, I tried 
> mri_surf2vol, however, it needs register.dat. As I understood, the 
> data.lh.mgh was already registered to fsaverage surface, so how can I 
> get the required register.dat file? Thank you for your attention.
>
> Best,
> Xiangyu
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?

2012-04-23 Thread Long 
Hi Douglas,

I tried to do spatial normalization for volume data, all steps are
following:

1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s subj01
--init-fsl --reg bb_register.dat

I checked the result by tkregister2, it looked good.

2) mris_preproc --target fsaverage --hemi lh --iv fsubj01_001.hdr
bb_register.dat --projfrac 0.5 --out lh.zmap.mgh

3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity fsaverage
--outvol subj01_001.nii.gz --projfrac 0.5 --fillribbon --template
wfrest_res_co_001.hdr

However, the output file subj01_001.nii.gz showed wrong orientation when
viewing in MRIcron, the image looked rotated. Could you please help with it?

Best,
Xiangyu

On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve
wrote:

> Hi Xiangyu, just add  --identity fsaverage  to the surf2vol command line
> doug
>
>
> On 04/19/2012 05:57 PM, Long wrote:
> > Hi all,
> >
> > I had a question when convert a surface to volume space.
> >
> > First, I converted a volume nifti data to fsaverage:
> >
> > mris_preproc --target fsaverage --hemi lh --iv data.nii
> > bb_register.dat --out data.lh.mgh
> >
> > Then, I want to convert the data.lh.mgh to volume space, I tried
> > mri_surf2vol, however, it needs register.dat. As I understood, the
> > data.lh.mgh was already registered to fsaverage surface, so how can I
> > get the required register.dat file? Thank you for your attention.
> >
> > Best,
> > Xiangyu
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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.
>
>
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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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Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?

2012-04-24 Thread Douglas N Greve 
How does it look in tkmedit?

On 04/23/2012 12:20 PM, Long wrote:
> Hi Douglas,
>
> I tried to do spatial normalization for volume data, all steps are 
> following:
>
> 1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s subj01 
> --init-fsl --reg bb_register.dat
>
> I checked the result by tkregister2, it looked good.
>
> 2) mris_preproc --target fsaverage --hemi lh --iv fsubj01_001.hdr 
> bb_register.dat --projfrac 0.5 --out lh.zmap.mgh
>
> 3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity fsaverage 
> --outvol subj01_001.nii.gz --projfrac 0.5 --fillribbon --template 
> wfrest_res_co_001.hdr
>
> However, the output file subj01_001.nii.gz showed wrong orientation 
> when viewing in MRIcron, the image looked rotated. Could you please 
> help with it?
>
> Best,
> Xiangyu
>
> On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Xiangyu, just add  --identity fsaverage  to the surf2vol
> command line
> doug
>
>
> On 04/19/2012 05:57 PM, Long wrote:
> > Hi all,
> >
> > I had a question when convert a surface to volume space.
> >
> > First, I converted a volume nifti data to fsaverage:
> >
> > mris_preproc --target fsaverage --hemi lh --iv data.nii
> > bb_register.dat --out data.lh.mgh
> >
> > Then, I want to convert the data.lh.mgh to volume space, I tried
> > mri_surf2vol, however, it needs register.dat. As I understood, the
> > data.lh.mgh was already registered to fsaverage surface, so how
> can I
> > get the required register.dat file? Thank you for your attention.
> >
> > Best,
> > Xiangyu
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
> ___
> 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.
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?

2012-05-14 Thread Douglas N Greve 
I don't know what that means. It is not an FS issue, it is something 
wrong on your system.
doug

On 05/14/2012 06:17 AM, Long wrote:
> Hi Douglas,
>
> I used the command:
>
> tkmedit fslt1mnifs orig.mgz ./lh.zmap.mgh
>
> but it said: Resource temporarily unavailable.
>
> Best,
> Xiangyu
>
> On Tue, Apr 24, 2012 at 5:01 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> How does it look in tkmedit?
>
>
> On 04/23/2012 12:20 PM, Long wrote:
>
> Hi Douglas,
>
> I tried to do spatial normalization for volume data, all steps
> are following:
>
> 1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s
> subj01 --init-fsl --reg bb_register.dat
>
> I checked the result by tkregister2, it looked good.
>
> 2) mris_preproc --target fsaverage --hemi lh --iv
> fsubj01_001.hdr bb_register.dat --projfrac 0.5 --out lh.zmap.mgh
>
> 3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity
> fsaverage --outvol subj01_001.nii.gz --projfrac 0.5
> --fillribbon --template wfrest_res_co_001.hdr
>
> However, the output file subj01_001.nii.gz showed wrong
> orientation when viewing in MRIcron, the image looked rotated.
> Could you please help with it?
>
> Best,
> Xiangyu
>
> On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>Hi Xiangyu, just add  --identity fsaverage  to the surf2vol
>command line
>doug
>
>
>On 04/19/2012 05:57 PM, Long wrote:
> > Hi all,
> >
> > I had a question when convert a surface to volume space.
> >
> > First, I converted a volume nifti data to fsaverage:
> >
> > mris_preproc --target fsaverage --hemi lh --iv data.nii
> > bb_register.dat --out data.lh.mgh
> >
> > Then, I want to convert the data.lh.mgh to volume space, I tried
> > mri_surf2vol, however, it needs register.dat. As I
> understood, the
> > data.lh.mgh was already registered to fsaverage surface, so how
>can I
> > get the required register.dat file? Thank you for your
> attention.
> >
> > Best,
> > Xiangyu
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>--
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
>Phone Number: 617-724-2358 
> >
>Fax: 617-726-7422   >
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
>FileDrop:
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> 
>
>___
>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.
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>

-- 
Douglas N. Greve,