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In addition, in my mri_vol2surf result, there are 35.5% vertices that are assigned 0 in all time frames. Then I checked its previous registration result and found that most parts of the brain are registered but I could also see some parts are not matched in some view. I attached a snapshot below for your reference, where the blue points are fMRI data. In the axial view, there is still a rotation between the functional and the anatomical volumes. 

So I am wondering is the ratio of the vertices with 0 values in all time frame in my result reasonable and how could I reduce that? fMRI resolution: 2mm*2mm*2mm / anatomical MRI resolution: 1mm*1mm*1mm  

Many thanks.

Best,
An

image.png


An <annaqu1024@gmail.com> 于2019年11月14日周四 上午10:47写道：
Oops sorry for the mistakenly reply. I will pay more attention in the future.

Bert is the folder with the anatomical data. I tried the following steps with the 4D volume but failed. Then I checked the registration result after bbregister and found that the volume was not registered. After that I tried another 4D volume to do the steps and successfully got the sampled intensity onto the surface.

The difference between the new 4D volume I used and the previous one is that there are two transformation matrices between them. The 4D dataset that I previously used but failed is the volume already registered to its anatomical volume(by using others tools). The new 4D volume that I tried and succeed is the volume not registered. 

I have no idea why the 4D volume after the transformation would cause a failed result. Could you please let me know that?

Many thanks.

Best,
An

Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> 于2019年11月13日周三 下午12:20写道：
If you have an anatomical MR that you have run through recon-all, then
just use that one instead of bert in your steps below
ps. Please remember to post to the FS list and not to us personally

On 11/12/19 8:41 PM, an wrote:
>
>         External Email - Use Caution
>
> Many thanks.
>
> I got the 4D fMRI dataset from others and it is not raw data. In order
> to run mri_vol2surf, I need to calculate the register.dat for the
> required flag --srcreg so I tried in this way.
>
> FYI, the 4D fMRI dataset should have been registered with its
> anatomical MR volume by using other tools.
>
> For now I only ran the recon-all on its anatomical MR volume without
> running the functional stream as I don't have the raw data.
>
> Should I also run the raw fMRI data from scratch by using functional
> stream? Or if I can run mri_vol2surf independently, which command
> should I use to get a register.dat file?
> In addition, the intensity of the 4D fMRI dataset I have is between
> [-1, 1] and not integers, would this cause any problem?
>
> Best,
> An
>
>
> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>> Don't do the 1st step.
>> Why are you registering it to bert? I'm pretty sure bert did not
>> participate in your fmri study
>> When you run mri_vol2surf, it will probably work better with
>> --projfrac 0.5
>>
>> On 11/11/2019 1:32 PM, An wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Prof. Greve,
>>>
>>> Thanks for your reply and sorry for the confusion.
>>>
>>> I have a 4D fMRI dataset with 10 time frames, where the intensity of
>>> each voxel is between [-1,1] and not integers. I want to map the
>>> intensities of the volumes on its corresponding surface in order to
>>> get the functional values on each vertex in each frame. I have
>>> already run its corresponding anatomical image in freesurfer.
>>>
>>> To achieve it, I tried the following steps:
>>> 1. conform the fmri series by using mri_convert
>>> 2. register the fmri series with the anatomy image by using
>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg register.dat
>>> 3. assign values from volumes to each vertex by using mri_vol2surf:
>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>> register.dat --hemi lh
>>>     I also tried the -regheader in mri_vol2surf: mri_vol2surf --src
>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>
>>>
>>> The /4Dvol.nii /aligns very well with the orig.mgz in freeview. But
>>> after step2, the registered volume looks wrong. I am wondering could
>>> I use bbregister to register multi-frame fMRI series to a single
>>> volume?
>>> I also tried to use --regheader to replace the --srcreg file in
>>> mri_vol2surf as the output register.dat in step2 is wrong. But the
>>> output is still wrong.
>>>
>>> Many thanks.
>>>
>>> Best,
>>> An
>>>
>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>> <mailto:DGREVE@mgh.harvard.edu>> 于2019年11月11日周一 下午12:16写道：
>>>
>>>     When you say it is 4D, what do you mean? That each label has its
>>>     own frame?
>>>
>>>     On 11/6/19 5:59 PM, 曲岸 wrote:
>>>     >
>>>     >         External Email - Use Caution
>>>     >
>>>     > Hi there,
>>>     >
>>>     > I am working with creating a surface parcellation from a
>>>     volumetric
>>>     > parcellation and have some questions as follows:
>>>     >
>>>     > 1. If the volumetric parcellation is a labeled 4D multi-frame
>>>     dataset,
>>>     > could I still use the mris_sample_parc? Or could mri_vol2surf
>>>     get the
>>>     > sampled labels for every vertex?
>>>     >
>>>     > 2. For the 4D multi-frame dataset and mri_vol2surf output
>>>     results,
>>>     > which GUI should I use to visualize it? I tried freeview for 4D
>>>     > multi-frame dataset but it looks weird.
>>>     >
>>>     > 3. Is there any command to separate multi-frame volume to
>>>     single frame
>>>     > volumes?
>>>     >
>>>     > Many thanks!
>>>     >
>>>     >
>>>     > Best,
>>>     > An
>>>     >
>>>     > _______________________________________________
>>>     > Freesurfer mailing list
>>>     > Freesurfer@nmr.mgh.harvard.edu
>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
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>>>
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>>
>>
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