9 Mar
2018
9 Mar
'18
11:15 a.m.
You create it with bbregister. See the multimodal integration tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
On 3/6/18 6:36 PM, srishti goel wrote:
I am sorry but that is what I am unsure about it. I don't know how to obtain a registration matrix or which registration matrix to use for this.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Mon, Mar 5, 2018 at 3:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Why did you remove the registration file? --srcreg below On 02/28/2018 04:13 PM, srishti goel wrote: > Hello, > > Thank you so much! I used the following command as you said and got an > error : must specify a source registration file or --regheader > > mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze > --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 > > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> > skype: srishti.goel12 > > > On Wed, Feb 28, 2018 at 10:13 AM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > you need to add --trgsubject fsaverage to your mri_vol2surf > command line > > > On 2/27/18 12:23 PM, srishti goel wrote: >> Hello, >> >> We are trying to project a volume map onto a surface. Our network >> based volume map is a .vmp file and our surface is a nifti file. >> We were able to convert the volume maps from .vmp to nifti. >> Our volume map is: negative_allsocial_proportion.nii >> Our surface is: SN_like_cortical_lh.nii >> The output file is named: neg_allsocial.nii >> >> We are trying to use the following command to now project the >> volume map on surface and the issues we are facing are: >> 1) We are unsure of what the purpose of the registration file is >> and where in the mir_vol2surf command should we specify the surface >> 2) If it is a matrix for something related to the surface on >> which we want to project our volume then how should we go about >> obtaining the registration file appropriate for our comparison. >> >> _Command:_ >> mri_vol2surf --src negative_allsocial_proportion.nii --src_type >> analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o >> ./neg_allsocial.nii --projfrac 0.5 >> >> _Then to project it:_ >> tksurfer fsaverage lh inflated -ov neg_allsocail.nii >> >> >> >> _______________________________________________ >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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