External Email - Use Caution
Dear Bruce:
Sorry I forget to tell you I'm using the gifti format 40 subjects
dHCP data, so these are neonatal data, I guess existing atlas like
fsaverage may not work well. So I want to create my own reference
template and project the fMRI data on it. And I guess there should be
40 time series on each vertex on the template corresponding to each
subjects', and they come from mri_register or mri_surf2surf? However,
After that mail I found an atlas by (Bozek et al. 2018,
https://brain-development.org/brain-atlases/atlases-from-the-dhcp-project/cortical-surface-atlas-bozek/).
The problem is about two main points: (1). Project my fMRI data from
individual subject to template. (2). The vertex number is large
(~6k-10k), so I want to downsample the atlas and then do the register
but I don't clearly know how to do.
(1). If I focus on the existing atlas by Bozek et al, Can I use
mris_convert to convert them into Freesurfer format and downsample it
to ~10% of the vertex and then register each of my subject's time
series onto it? If yes, is mris_decimate and then mri_surf2surf should
be the right command?
(2). If I still want to create my own template. After generated
lh.wholebrain.tif, and I get lh.sphere.reg for each subject. Then I
think I could use mri_surf2surf to map the individual fMRI to the
template? Am I doing the right thing? And when and how should I do the
downsample?
Really sorry for not clearly described my question in last mail!
Still looking forward to hear your reply, thank you!
Best wishes,
Jingyue Zhang
Bruce Fischl <fis...@nmr.mgh.harvard.edu> 于2019年5月28日周二 下午10:52写道：
> Hi Jingyue
>
> can you explain what your goal is in a bit more detail? My guess is you
> can use the existing atlas/template and not create a new one.
>
> As for the gifti conversion, I think mris_convert can handle it
>
> cheers
> Bruce
> On Tue, 28
> May
> 2019, Jingyue Zhang wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts: Hello! I'm a new student to surface based
> > fMRI analysis. Now I'm dealing with a functional parcellation problem.
> The
> > subjects in my dataset has different vertex number and I need to do a
> group
> > level parcellation, so I decided to make a group reference template.
> > My step is almost following thispost:
> https://www.mail-archive.com/freesurfer@surfer.nmr.mgh.harvard.edu/ms
> > g00420.html ,the lh.wholebrain.tif and lh.sphere.reg for two test
> subjects
> > have successfully generated. But I'm still wondering about these files
> and
> > what to do next to get my individual fMRI time series on vertex
> registerd to
> > the template.
> > The second question is, the vertex number (~100000) is much more
> > than my voxel based masked data (~50000). Neither is easy to do the
> > susequent analysis efficiently. So how should I correctly downsample it?
> > Should I downsample the template or downsample my surface before making
> > template? Will mris_decimate work?
> > The last question is my subject has gifti format sulc and curv
> data
> > (.shape.gii). I have tried to use MRI_read and MRI_write to write to an
> .mgh
> > file and add -sulc sulc.mgh for each command and they seems worked. Can I
> > convert them to file like .sulc? Or just keep the .mgh and -sulc
> sulc.mgh is
> > OK?
> > I'm looking forward to hear your reply! Really thanks for your
> help!
> >
> > Best wishes,
> > Jingyue Zhang
> >
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