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. <dgr...@mgh.harvard.edu<mailto:dgr...@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
>
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