why not just map the fmri volume into the anatomical volume
(mri_vol2vol)? Why go through the surface at all?

On 4/3/19 12:34 PM, Zhi Li wrote:
>
>         External Email - Use Caution
>
> 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
> <mailto: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 <mailto: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>
>         <mailto: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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