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Hi Doug,

I think I might have some gaps in my knowledge regarding the type of surface 
spaces Freesurfer uses and can produce, so I wanted to make sure that I got 
everything right. So my belief is that Freesurfer has the conformed surfaces 
which represent subjects' native topography, but they are built from the 
isotropic version of the images (orig.mgz) and these are actually the default 
outputs of Freesurfer. Then, we can produce the native space surfaces in the 
native T1 resolution which follows the original xyz coordinates by following 
the commands mentioned on the FSAnat to NativeAnat page using the rawavg.mgz. 
Finally, we have the standard template spaces such as fsaverage which the 
spheres that are created from the conformed surfaces are registered to.

One thing I forgot to mention about the data I have is that my EPI images are 
in the same space with my T1 images, but they keep their original resolution. 
Do I need to resample them in order to map them to any of these surface spaces 
? If that is the case, I believe depending on the surface space I want to end 
up with I also should use different target images for this resampling. For 
instance, if I want to create maps in the conformed surfaces, I need to 
resample them to the resolution of my orig.mgz and for the native surfaces, I 
should use the rawavg.mgz. Am I right about all these ? If so, I think I now 
know how to approach this a little bit better.

Best,
Ozzy


________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve 
<dgr...@mgh.harvard.edu>
Sent: Monday, May 18, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Volume timeseries to native and fsaverage

oh, if you want them in conformed space, they are already there

On 5/18/2020 11:34 AM, özenç taşkın wrote:

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Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz 
with tkregister2 instead of rawavg.mgz if the aim is to get surface maps in 
native space, am I right ? And by native space I mean the subjects' native 
brain structure and not necessarily the native xyz coordinates (I guess 
conformed space is the right term for this, but I am not sure).

Best,
Ozzy

________________________________
From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, May 13, 2020 3:07 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Volume timeseries to native and fsaverage



On 5/11/2020 5:53 PM, özenç taskin wrote:

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Hello Freesurfer developers,

I am trying to map a 4D volumetric EPI image between different surfaces and I'd 
like a little bit of guidance as I am slightly confused about some of the 
outputs of freesurfer.

I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd 
like to map this timeseries image to subject's native surface. Here is how I am 
currently doing this operation:

1 - Create a register.dat by using fsl identity matrix since I am already in 
the native space:
tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit 
--reg <register.dat>
This is ok, but unnecessary. You can use --regheader subject in mri_vol2surf 
below instead of --reg
2 - Then, using this register.dat to make surfaces from the 4D timeseries with:
mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o 
<output_surface.mgz>
Add --projfrac 0.5 to sample in the middle of the ribbon.
I used these functions in the past to map statistical images to surface, but it 
might not be the right thing to do for timeseries in which case please let me 
know. Assuming this is correct though, next I want to move this native surface 
timeseries to fsaverage surface. I am pretty sure the calculations are in 
there, but I am not really sure which ones I need to use and with which 
freesurfer commands I can do this.
Time series are no different than a single frame. You can actually map directly 
to fsaverage in mri_vol2surf with --trgsubject fsaverage (or you can take the 
vol2surf output and run mri_surf2surf on it)

Lastly, I came across this freesurfer page 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks 
about fsaverage to native surface conversion and the examples there made me a 
bit confused. Aren't the surface files in the surf directory (e.g lh.pial, 
lh.inflated) already in the native space ? Do I need to create a lh.pial.native 
using these commands to overlay my timeseries image ?
No, you do not. That page just talks about if you want an actual surface file 
with xyz in the native coordinates. You do not need to have this file.

Best,
Ozzy






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