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
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
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 greve@nmr.mgh.harvard.eduwrote:
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 greve@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.
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:
- 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.
- mris_preproc --target fsaverage --hemi lh --iv fsubj01_001.hdr
bb_register.dat --projfrac 0.5 --out lh.zmap.mgh
- 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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
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Douglas N Greve -
Long