I'm still confused as to what you are trying to do. If you just want to
sample your data onto the surface, then you do not need to resample it
at all. You just run mri_vol2surf with the appropriate registration and
projection fraction. If I'm misunderstanding, please clarify.
On 5/19/2020 4:27 PM, özenç taşkın wrote:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
