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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@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