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:

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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.edumailto: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:

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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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