Hi Greg, yes, that sounds correct cheers Bruce On Mon, 29 Oct 2018, GREGORY R KIRK wrote:
External Email - Use Caution there is some misunderstanding ? I said to resample onto the cortical surface not into a volume you say Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). but this is not mri_vol2surf mri_vol2surf does not have --s as an option. the volume is already in registration with orig.mgz for the subject so i can't use --reg register.dat I need to use an identity transformation somehow. i tried mri_vol2surf --mov vout.mgz --regheader 311140 --hemi lh --o R1.mgz and that seemed to work, is this correct ? greg ____________________________________________________________________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> Sent: Monday, October 22, 2018 11:58:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] resampling data onto cortical surface Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1. On 10/22/2018 12:55 PM, GREGORY R KIRK wrote: > > External Email - Use Caution > > > I have R1 values that I want to resample onto the cortical surface. > The R1 values were computed from a multi echo > > T1 sequence that was also used to create the T1 weighted image that > was used in recon-all to produce the cortical surface reconstructions > > and thus is inherently in registration to the 001.mgz that was used to > start recon. There will be a difference in orientation in the volume > > in that orig.mgz is in coronal and in the .mgz format. > > > I was thinking that if I run the first step of recon-all it should > give me an volume named orig.mgz that is in registration to the > freesurfer space > > for the subject ... or else some call to mri_convert reslice_as or > whatever is used in the recon-all script to convert 001.mgz to orig.mgz > > > > > then my problem is to get a file with the resampling of the R1 onto > the cortical surface withR1 values at each vertex. > > > when i work with fmri data I run bbregister and get the transformation > from the epi volume to the freesurfer space and then use > > mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface > --reg bb.register.dat \ > --projfrac 0.5 --interp nearest \ > --hemi lh --o lh.sig.mgh > > to resample the epi data onto the cortical surface. however in this case the R1 data > is already in perfect registration to the T1 other than the reorientation and reslicing > done to prepare the orig.mgz volume. > > so can someone tell me what is the proper way to cook this goose > > Greg > > > > _______________________________________________ > 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
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