Re: [Freesurfer] Map fMRI data onto surface

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Hi Prof. Greve,

Thanks for your help. Now I can successfully map the time frames intensities onto the surface without 0 value. The problem is that I used the wrong input data. What I got from others is a preprocessed fMRI data by using other tools and it is a set of points instead of a grayscale image. I got the raw data today and finally it mapped onto surface correctly.

Thanks again for your help!

Best, An

An annaqu1024@gmail.com 于2019年11月21日周四 下午4:35写道：

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: image.png]

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

...

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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.png 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. <DGREVE@mgh.harvard.edu
<mailto:DGREVE@mgh.harvard.edu>
> <mailto: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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