On 07/02/2012 12:01 PM, Luis R. Piloto wrote: > Hi Doug, > > Thanks for getting back to me. I'm right around the vicinity of my desired > results, but had just three more questions. > > 1) When running the mri_vol2surf command and specifying --reg, is there any > way I can pass in a registration file generated by FSL's flirt command (i.e. > flirt -in functional.nii -ref structurual.nii.gz ... -omat functional.mat, > where functional.mat is the registration file from my functional to my > structural) Currently, I'm using a register.dat file generated by > bbregister, but I'd rather use the flirt outputted regustration file because > it's being used in other parts of my pipeline. Is there perhaps a way to > convert from the flirt output to a register.dat file? I thought using > bbregister with init-fsl might let me specify a flirt registration file, but > this was not the case. You can convert it with something like tkregister2 --mov example_func.nii.gz --fsl fsl.mat --s subject --reg reg.fsl.dat > > 2) To the best of my understanding, when used on functional data and > outputting to .w files (and subsequently viewing the .w file in ascii form), > the mri_vol2surf command generates a surface file where each vertex has > attached to it a weight corresponding to the functional activity. However, > how does this work when I use a 4D functional file as input? I'd expect the > same sort of output, but instead each vertex would have a series of weights > (instead of just a single weight) corresponding to the functional activity at > each timepoint. Even when I output to a .mgh file while using a 4D volume > with mri_vol2surf and overlay the resulting .mgh file in tksurfer, it still > seems like there is only one "weight" for each vertex. Am I missing > something? It should output a series of weights if the input has multiple "frames". Check the input and output with mri_info. Don't use .w files, they only support one frame (and we're trying to phase them out). > > 3) Is there a way to overlay the resulting .mgh (or .w or .asc) from > mri_vol2surf in freeview? Yes. I don't know off the top of my head. Maybe another from the FS team can chime in. doug > > Thanks again for all of your help. > > Regards, > Luis > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Jun 2012 12:54:20 -0400 > From: Douglas N Greve<gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_vol2surf and Spherical Surfaces > To: freesurfer@nmr.mgh.harvard.edu > Message-ID:<4fe9e93c.3090...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Luis, yes there is a more efficient way. Specify the native res > functional as the --mov argument and specify the registration that you > used to create the hires_functional as the --reg argument (instead of > --regheader). While you can use a .w file, I would recommend instead a > .mgh file (we're trying to phase out the .w); If you use mgh format, not > need to spec a --out_type. That command will convert to the native > subject surface. If you want to go to fsaverage you can either run > mri_surf2surf after that or spec --trgsubject fsaverage > doug > > On 06/25/2012 03:43 PM, Luis R. Piloto wrote: >> Hello Fellow Freesurfers, >> >> I need some verification that my method for mapping functional data onto a >> spherical surface is sound. >> >> What I'm currently doing is running recon-all on my high-resolution, >> structural volume (.nii.gz format). After that, I take a single timepoint >> of my functional data (that has been both registered and upsampled to the >> high-res structural space), and run it through mri_vol2surf with the >> following command: >> mri_vol2surf --mov highres_functional_slice00.niii.gz --hemi lh --regheader >> my_subject_name --out_type paint -o ./my_output_surface.w >> >> What I'm most worried about is whether this method of registration (i.e. >> specifying --regheader) is sufficient to go from the upsampled/registered >> functional to the surface? Also is there some more efficient way of doing >> this? I feel like there might be a smarter way to go from the functional to >> the structural without having to explicitly register and upsample before >> using mri_vol2surf. >> >> After this step, I simply pass my_output_surface.w to a program that reads >> the corresponding vertex and functional activity at that location and look >> up the vertex coordinates in my lh.sphere file. Any feedback would be >> really appreciated as I'm still really new to this software suite and was >> given a highly specific task to take care of. Thanks in advance! >> >> Regards, >> Luis Piloto >> >> >> _______________________________________________ >> 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.
