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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: image.png]
Greve, Douglas N.,Ph.D. DGREVE@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 CautionHi 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:
- ran recon-all on its anatomical volume.
- 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
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