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:
>
>         External Email - Use Caution
>
> 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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