Re: [Freesurfer] Map fMRI data onto surface

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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: image.png] [image: image.png]

Greve, Douglas N.,Ph.D. DGREVE@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:

...

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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.png

Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto: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 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
>
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