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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
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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