Can I display register.dat in tksurfer? Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: that writes the file named register.dat that has the affine registration matrix (and some other things) On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > Here it is: > > bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz > --reg register.dat --bold --init-header > > -jason. > > On 05/02/2011 00:18, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > can you send us your command line? > On Sat, 5 Feb 2011, Jason Connolly wrote: > >> Hi Doug, >> >> I am now at the bbregister stage ... I ran this but it is not clear to me >> where the output is? I don't see an output flag ... >> >> Can you tell me where to look for my output? >> >> Almost there! >> >> Many thanks, Jason. >> >> >> On 04/02/2011 23:49, "Jason Connolly" <jason.conno...@newcastle.ac.uk> wrote: >> >> Thank you. -jason. >> >> >> On 04/02/2011 23:48, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >> >> You can load in the functional with MRIread since you are going to be >> replacing all the pixel data anyway with your single time point. Just >> use the single argument. The second is if you dont want to read in the >> pixel data. >> >> Jason Connolly wrote: >>> Thanks. >>> >>> So, to clarify, I am trying to just make an overlay. So do I use MRIread >>> with a functional .img as input? >>> >>> Is the second argument in MRIread my scanCoords for my phase-value pixels? >>> >>> Almost there ... >>> >>> >>> >>> >>> On 04/02/2011 23:35, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >>> >>> It's the vol field. >>> doug >>> >>> Jason Connolly wrote: >>> >>>> Hi Doug, >>>> >>>> You state: >>>> >>>> "then replace the pixel data with your >>>> analyzed data" >>>> >>>> I cannot seem to find the field for the pixel data. Can you tell me where >>>> to position these values? >>>> >>>> Thanks! -jason. >>>> >>>> >>>> On 04/02/2011 18:15, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >>>> >>>> You should save it out as nifti (see MRIwrite.m and MRIread.m). I would >>>> suggest using MRIread.m to read in your file in order to create the >>>> proper header information, then replace the pixel data with your >>>> analyzed data, then use MRIwrite.m to save it out. Then use bbregister >>>> to register this volume to the anatomical, then use mri_vol2surf to >>>> sample it to the surface (either native anatomical or to some other >>>> subject). >>>> >>>> doug >>>> >>>> Jason Connolly wrote: >>>> >>>> >>>>> Dear freesurfer experts: >>>>> >>>>> I have been using matlab to analyze a retinotopic dataset. >>>>> >>>>> However, the 3D volumes are not in standardized space (and I wish to >>>>> display multiple maps from different subjects on one surface). >>>>> >>>>> Although the initial segmentations were done in freesurfer, my question >>>>> is: >>>>> >>>>> Is it possible to take matlab arrays that contain 3D space anatomical >>>>> coordinates and phase information (on a voxel by voxel basis) and display >>>>> these on a standardized inflated freesurfer-generated surface? >>>>> >>>>> If so, is the pipeline documented? >>>>> >>>>> Many thanks, >>>>> >>>>> Jason. >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> >>>> 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, 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 >> >> >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
