I would just do mri_vol2vol --i vin.nii --regheader --targ orig.mgz --o vout.mgz
On 10/22/2018 05:52 PM, GREGORY R KIRK wrote: > > External Email - Use Caution > > thanks Doug, one more thing to make sure I get it correct. > > > If I have a volume of quantitative MR volumes in the native space of > the T1 and I want them to be in registration with the freesurfer space > > of this subject I woiuld > > > mri_convert -it nii -ot mgz vin.nii vout.mgz and then > > mri_convert vout.mgz vc.mgz --conform --no_scale --nochange > > > so that it is in the freesurfer space but not scaled and not changed > from float to uchar, correct ? > > > thanks > > > 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 > > > _______________________________________________ > 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
