What is the blue? The best way to dispaly it is to show the fMRI in gray scale with the surfaces overlaid on it. What exactly is the input pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz? How was it created? Can you verify that the orientation is correct? You can load it in FreeView
On 11/21/19 4:35 PM, An wrote: > > External Email - Use Caution > > Hi Prof. Greve, > > Thanks for the correction. Here are the results when I ran bbregister > with --t2. It's still does not well registered. The log file is > attached in this email. > > Also, I was just informed that the fMRI 4D series and the MRI are not > scanned in the same day. Is it possible to register them in freesurfer. > > 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3:54写道： > > 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> > > <mailto: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>> > > > <mailto: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>> > > > <mailto: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>> > > <mailto: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> > <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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
