Re: [caret-users] volume data corresponding to the MNI surface data
Hi Zhuangming, This option can be handy, but in this context, it's important to keep your expectations modest, and be aware of the limitations, because the odds of the resulting ROI/label/paint volume aligning nicely with whatever you want it to (surface or other anatomical/functional volume) are not as high as I'd like them to be. And there is a good chance there are surface-based methods to do your analysis that might be more accurate. If you still want to project surface-to-volume, then download the template from MNI using the link below, and select mni_icbm152_t1_tal_nlin_sym_09a.nii using the feature that lets you select the stereotaxic space for your projection by selecting a volume. The capture I sent earlier shows decent alignment between this volume and the MNI surface. If there is an anatomical volume that aligns better with data you want to use with the resulting ROI volume, then you could also use that volume's stereotaxic space, but first make sure the MNI surface aligns well with it using the D/C: Volume outline/contours featuer (whatever is the last tab on the drop-down menu, when you have a volume loaded). Donna On Mar 20, 2014, at 8:54 PM, 沈庄明 wrote: > Hi Donna, > > Thanks for your response. I have a paint type data in MNI space. The data > corresponds to the surface with 40962 nodes. Actually, I want to convert the > surface-based paint type data to a volume-based paint type data. I found > Caret could do the task by "Copy Surface Paint Column to Paint Volume", but I > need to select the volume space. So I hope you could give me some advice on > the selection. > Cheers, > > Zhuangming Shen > > > > -原始邮件- > > 发件人: "Donna Dierker" > > 发送时间: 2014年3月20日 星期四 > > 收件人: "Caret, SureFit, and SuMS software users" > > > > 抄送: > > 主题: Re: [caret-users] volume data corresponding to the MNI surface data > > > > This is a tough question that suggests that perhaps you are using > > MNI_surf_reg.RIGHT.40962.coord as a mapping substrate. It is possible the > > MNI/CIVET folks have a recommended method for doing this, but I'm afraid I > > don't know that it exists, much less be able to point you to it. (Someone > > else here might, though.) > > > > But if you're looking for something like that surface, in terms of the > > tighter sulcal/gyral alignment and a larger pool of subjects, then I would > > point you to Conte69 > > (http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas), > > simply because then I can say FNIRT is the right choice, because that is > > the spatial normalization method used to get those subjects into avg152T1 > > space. > > > > Could you provide more context for how you plan to use this surface? > > > > > > On Mar 20, 2014, at 1:36 AM, 沈庄明 wrote: > > > > > Hi Donna, > > > > > >Thanks for your prompt reply. By the way, which space (AFNI, FLIRT, > > > FLIRT-222, FNIRT, FNIRT-222, MRITOTAL, SPM, SPM95, SPM96, SPM2, SPM5, > > > T88, 711-2B, 711-2C, 711-2O, 711-2Y) should I choose for > > > mni_icbm152_t1_tal_nlin_sym_09a.nii ? Thanks again! > > > > > >Cheers, > > > > > > Zhuangming > > > > > > > > > -原始邮件- > > > 发件人: "Donna Dierker" > > > 发送时间: 2014年3月20日 星期四 > > > 收件人: "Caret, SureFit, and SuMS software users" > > > > > > 抄送: > > > 主题: Re: [caret-users] volume data corresponding to the MNI surface data > > > > > > Hi Zhuangming, > > > > > > The mni_icbm152_t1_tal_nlin_sym_09a.nii file in this MNI template aligns > > > pretty well with the MNI surface: > > > > > > http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_nifti.zip > > > > > > See attached capture. The underlay is the above T1 volume. Two surface > > > contours are overlaid: > > > > > > blue - MNI_surf_reg.RIGHT.40962.coord > > > red - > > > PALS_Human.PALS.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.REG-with-MNI_surf_reg.40962.coord > > > > > > The MNI surface was generated on the CIVET mesh from a population of 152 > > > subjects. The PALS surface was generated on the 74k_palsb12 mesh from a > > > population of 12 subjects. Not surprisingly, the MNI surface aligns > > > better with the MNI T1 template. There is a mean volume for the PALS > > > surface, but I'm guessing you are more interested in the MNI te
Re: [caret-users] volume data corresponding to the MNI surface data
Hi Donna, Thanks for your response. I have a paint type data in MNI space. The data corresponds to the surface with 40962 nodes. Actually, I want to convert the surface-based paint type data to a volume-based paint type data. I found Caret could do the task by "Copy Surface Paint Column to Paint Volume", but I need to select the volume space. So I hope you could give me some advice on the selection. Cheers, Zhuangming Shen > -原始邮件- > 发件人: "Donna Dierker" > 发送时间: 2014年3月20日 星期四 > 收件人: "Caret, SureFit, and SuMS software users" > > 抄送: > 主题: Re: [caret-users] volume data corresponding to the MNI surface data > > This is a tough question that suggests that perhaps you are using > MNI_surf_reg.RIGHT.40962.coord as a mapping substrate. It is possible the > MNI/CIVET folks have a recommended method for doing this, but I'm afraid I > don't know that it exists, much less be able to point you to it. (Someone > else here might, though.) > > But if you're looking for something like that surface, in terms of the > tighter sulcal/gyral alignment and a larger pool of subjects, then I would > point you to Conte69 > (http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas), > simply because then I can say FNIRT is the right choice, because that is the > spatial normalization method used to get those subjects into avg152T1 space. > > Could you provide more context for how you plan to use this surface? > > > On Mar 20, 2014, at 1:36 AM, 沈庄明 wrote: > > > Hi Donna, > > > >Thanks for your prompt reply. By the way, which space (AFNI, FLIRT, > > FLIRT-222, FNIRT, FNIRT-222, MRITOTAL, SPM, SPM95, SPM96, SPM2, SPM5, T88, > > 711-2B, 711-2C, 711-2O, 711-2Y) should I choose for > > mni_icbm152_t1_tal_nlin_sym_09a.nii ? Thanks again! > > > >Cheers, > > > > Zhuangming > > > > > > -----原始邮件- > > 发件人: "Donna Dierker" > > 发送时间: 2014年3月20日 星期四 > > 收件人: "Caret, SureFit, and SuMS software users" > > > > 抄送: > > 主题: Re: [caret-users] volume data corresponding to the MNI surface data > > > > Hi Zhuangming, > > > > The mni_icbm152_t1_tal_nlin_sym_09a.nii file in this MNI template aligns > > pretty well with the MNI surface: > > > > http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_nifti.zip > > > > See attached capture. The underlay is the above T1 volume. Two surface > > contours are overlaid: > > > > blue - MNI_surf_reg.RIGHT.40962.coord > > red - > > PALS_Human.PALS.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.REG-with-MNI_surf_reg.40962.coord > > > > The MNI surface was generated on the CIVET mesh from a population of 152 > > subjects. The PALS surface was generated on the 74k_palsb12 mesh from a > > population of 12 subjects. Not surprisingly, the MNI surface aligns better > > with the MNI T1 template. There is a mean volume for the PALS surface, but > > I'm guessing you are more interested in the MNI template. > > > > This spec file has both the MNI and PALS mean midthickness surfaces, > > because it shows the results of registering one atlas to the other. > > > > Donna > > > > > > On Mar 19, 2014, at 2:09 AM, 沈庄明 wrote: > > > >> Hi everyone, > >> I found a human surface data in MNI space > >> (MNI_surf_reg.BOTH.REG-with-PLAS.40962.spec) at > >> http://sumsdb.wustl.edu/sums/directory.do?id=6656001&dir_name=MNI_surf_reg. > >> Is the volume data (i.e. the T1-weighted image) corresponding to the > >> human surface data available? Thanks! > >> Cheers, > >> > >> Zhuangming Shen > >> > >> > >> > >> > >> > >> > >> ___ > >> caret-users mailing list > >> caret-users@brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] volume data corresponding to the MNI surface data
This is a tough question that suggests that perhaps you are using MNI_surf_reg.RIGHT.40962.coord as a mapping substrate. It is possible the MNI/CIVET folks have a recommended method for doing this, but I'm afraid I don't know that it exists, much less be able to point you to it. (Someone else here might, though.) But if you're looking for something like that surface, in terms of the tighter sulcal/gyral alignment and a larger pool of subjects, then I would point you to Conte69 (http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas), simply because then I can say FNIRT is the right choice, because that is the spatial normalization method used to get those subjects into avg152T1 space. Could you provide more context for how you plan to use this surface? On Mar 20, 2014, at 1:36 AM, 沈庄明 wrote: > Hi Donna, > >Thanks for your prompt reply. By the way, which space (AFNI, FLIRT, > FLIRT-222, FNIRT, FNIRT-222, MRITOTAL, SPM, SPM95, SPM96, SPM2, SPM5, T88, > 711-2B, 711-2C, 711-2O, 711-2Y) should I choose for > mni_icbm152_t1_tal_nlin_sym_09a.nii ? Thanks again! > >Cheers, > > Zhuangming > > > -原始邮件- > 发件人: "Donna Dierker" > 发送时间: 2014年3月20日 星期四 > 收件人: "Caret, SureFit, and SuMS software users" > > 抄送: > 主题: Re: [caret-users] volume data corresponding to the MNI surface data > > Hi Zhuangming, > > The mni_icbm152_t1_tal_nlin_sym_09a.nii file in this MNI template aligns > pretty well with the MNI surface: > > http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_nifti.zip > > See attached capture. The underlay is the above T1 volume. Two surface > contours are overlaid: > > blue - MNI_surf_reg.RIGHT.40962.coord > red - > PALS_Human.PALS.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.REG-with-MNI_surf_reg.40962.coord > > The MNI surface was generated on the CIVET mesh from a population of 152 > subjects. The PALS surface was generated on the 74k_palsb12 mesh from a > population of 12 subjects. Not surprisingly, the MNI surface aligns better > with the MNI T1 template. There is a mean volume for the PALS surface, but > I'm guessing you are more interested in the MNI template. > > This spec file has both the MNI and PALS mean midthickness surfaces, because > it shows the results of registering one atlas to the other. > > Donna > > > On Mar 19, 2014, at 2:09 AM, 沈庄明 wrote: > >> Hi everyone, >> I found a human surface data in MNI space >> (MNI_surf_reg.BOTH.REG-with-PLAS.40962.spec) at >> http://sumsdb.wustl.edu/sums/directory.do?id=6656001&dir_name=MNI_surf_reg. >> Is the volume data (i.e. the T1-weighted image) corresponding to the human >> surface data available? Thanks! >> Cheers, >> >> Zhuangming Shen >> >> >> >> >> >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] volume data corresponding to the MNI surface data
Hi everyone, I found a human surface data in MNI space (MNI_surf_reg.BOTH.REG-with-PLAS.40962.spec) at http://sumsdb.wustl.edu/sums/directory.do?id=6656001&dir_name=MNI_surf_reg. Is the volume data (i.e. the T1-weighted image) corresponding to the human surface data available? Thanks! Cheers, Zhuangming Shen ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
