Re: [Freesurfer] resampling data onto cortical surface

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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:

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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

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