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Hello!
You are right I ran second-level analysis in FSL and so the gfeat results are in volume space. However, I used the participant's T1 as the standard space (instead of using MNI), so the gfeat maps are still in the native T1. In this case I don't think I need to recon-all the template brain. But how would I view things on surface in any case?
Thank you!
Yuqi
-----原始邮件-----
发件人:"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
发送时间:2021-12-13 10:13:31 (星期一)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Overlaying gfreat results to surface
OK, it's been a while since I've done this, best answers below
On 12/9/2021 4:43 AM, 刘宇琦 wrote:
Did you sample the first level onto the surface and then run the gfeat analysis in surface space?External Email - Use Caution
Hi Freesurfer experts:
I have a question on displaying results from FSL FEAT on surface reconstructed by freesurfer, especially results from higher-level analysis from gfeat directories.
So I have successfully done recon-all on the participant's T1. I've also performed both first-level and higher-level analyses in FEAT. In overlaying first-level results from .feat directories, I did the following:
reg-feat2anat --feat sub1_run1.feat --subject sub1
feat2surf --feat featdir
Then, I overlaid the zstat1.mgh generated by the second command to surface, applying the anat2exf.register.dat file generated by the first command. It all worked fine.
However, I'm not sure how to overlay zstat1.nii.gz from higher-level analyses (.gfeat/cope1.feat/stats/) to surface. According to online tutorials I found below, I could overay the zstat1.nii.gz file to surface, applying the anat2std.register.dat file from the first command above.
It looks like the answer to the above question is "no". It looks like you have just done a typical gfeat analysis in the volume. Is this what you wanted? If so, you can still view things on the surface, but you have to run recon-all on the template volume (is it mni152?).
But it didn't work. The figure on the left below shows results on 3D volume space and the figure on the right shows z values on surface using the method above. However, nothing showed up on surface and the values shown in the Config window are weird. My guess is that I have to first convert zstat1.nii.gz to zstat1.mgh and then apply registration, but I'm not exactly sure. Can anyone give any instructions?
My other question is that the oneline tutorials on this issue use tkmedit and tkregister2 tools to inspect registration from feat to surface. However, none of these commands opens gui windows on my end. I'm using Ubuntu 18.04 on a Win10 and FreeSurfer 7. I guess these tools are replaced by Freeview but I don't know how to check feat2surf registration in Freeview. Can anyone provide some guidance?
Thank you,
Yuqi
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