Re: [Freesurfer] Transform functional surface data to volume

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Refer to my previous question. I found that 'vlrmerge' could be used to visualize the whole brain activation through mapping the left and right surface to the volume. But the data generated by vlrmerge cannot be used for analyzing. Hence I am wandering if there is a way to sample/map the 2D raw fmri time series to 3D volume?

On Wed, 3 Apr 2019 at 12:26, Zhi Li lizhi.psych@gmail.com wrote:

Sorry for my confusing explanation. I mean cortical grey matter. How could I map the left and right surface fmri data to volume? For example, how to transform the preprocessed left surface data 'fmcpr.odd.sm5.fsaverage.lh.nii.gz' to 3D volume?

Thanks,

Lizhi

On Wed, 3 Apr 2019 at 12:13, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

...

you mean just subcortical gray matter? You could map the aseg into the functional space with mri_label2vol (run with --help to get docs and examples). Then mri_binarize --i aseg.func.nii.gz --subcort-gm --o subcortgm.mgz, then mask the fmri time series (fmcpr.nii.gz) using mri_mask.

On 4/3/19 10:23 AM, Zhi Li wrote:

...

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I see and thank you very much. May I know If I could transform the surface-based time series data to volume space, like the space of subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get the whole brain 3D volume fmri data by changing the subcortical mask in folder 'mri.2mm' to the whole brain mask, but I do not need the part of white matter. See if it is applicable?

Thanks,

Lizhi

On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

On 4/2/19 4:23 PM, Zhi Li wrote:
>
>         External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I would like to transform the task-based surface data to volume.
May I
> know if it is applicable? I tried "mri_surf2vol --o test.nii.gz
> --subject sub002 --so fs/sub002/surf/lh.white
> fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my
system
> frozen. Any suggestions would be appreciated.
You are trying to convert the raw time series data into the
anatomical
space. The anat space is 256*256*256. If you have many time
points, the
functional volume in the anatomical space is going to be huge. This
would explain why your computer is frozen. Also, the surface fmri
data
is on subject fsaverage, not on sub002.
>
> Another problem is that in some individuals I found the RAS
> information of preprocessed surface data of different sessions
are not
> identical, that means the "voxel to ras transform" and "ras to
voxel
> transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different
between
> seesion1 (folder 001) and session2 (folder 002). May I know how
this
> happened and will it influence the final result? Should I keep

them

...

> the same?
The vox2ras for surface overlay data is not valid, so ignore it.
>
> Thanks,
>
> LIzhi
>
>
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