Why are you using --t1? If this is fmri, it should be --t2 On 11/21/19 3:27 PM, An wrote: > > External Email - Use Caution > > The image in the previous email uses the command tkregisterfv to > visualize the registration result after step2 bbregister, where I > uncheck the boxes of the surface layers. The full command of my > bbregister is: bbregister --mov fMRI.nii --s subjid --reg register.dat > --t1. > I attached both the registration result with checking the boxes of the > surface layers and my final result mapped onto surface below. > The log file is also attached to this email, please take a look at > your convenience. > > Many thanks. > > Best, > An > > image.png 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2:49写道： > > 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> > > <mailto: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> > > <mailto: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> > <mailto: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 <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
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