It is hard to say from that image, but it does not look registered to me. - your bbregister command is not valid as it is, please give the full command - please send the bbregister log file - to look at the registration, use tkregisterfv. It will show the surfaces over the fMRI
On 11/21/19 1:20 PM, An wrote: > > External Email - Use Caution > > Hi Prof. Greve, > > Thanks for your reply. I do it in the following steps: > 1. ran recon-all on the anatomical volume: recon-all -i MRI.nii -s > subjid -all > 2. register the fMRI series with the anatomical volume by using > bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat > 3. assign values from volumes to each surface vertex through the > command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz > --srcreg register.dat --hemi lh > > I also attached the registered image after step2. It looks like they > are not perfectly aligned. Is there anyway to improve that and also > the final result? > > Many thanks. > > Best, > An > image.png > > Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>> 于2019年11月21日周四 下午12:42写道： > > 35% sounds high to me. Did you actually check the registration > > You can always load the the fMRI as an overlay in freeview, try > tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz > Also, please include command lines you used > > On 11/21/19 10:03 AM, An wrote: > > > > External Email - Use Caution > > > > Hi there, > > > > I want to map the intensities of the fMRI 4D volumes onto its > surface > > in order to get the functional values on each vertex in each frame. > > > > I have done the following steps for achieving this: > > 1. ran recon-all on its anatomical volume. > > 2. register the fMRI series with the anatomical volume by using > > bbregister. > > 3. assign values from volumes to each surface vertex through the > > command mri_vol2surf. > > > > I have got a result of mapping the 4D volumes intensities onto its > > surfaces but there are 35.5% vertices assigned 0 value in every > time > > frame. > > > > I am wondering is the ratio reasonable and how could I improve the > > result? I guess resolution would be one of reasons causing the > high 0 > > value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. > > > > Many thanks for your help. > > > > Best, > > An > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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
