Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?
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 gr...@nmr.mgh.harvard.edu 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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 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 mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center
Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?
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 gr...@nmr.mgh.harvard.edu 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 mailto: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 mailto:gr...@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. -- 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
Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?
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.
Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?
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 gr...@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 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. ___ 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] How to convert a surface to volume space after using mris_preproc?
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 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.
