what do you mean by a voxel shift?

On 03/28/2016 04:03 PM, Ajay Kurani wrote:

Hi Freesurfer Experts, In testing mris_reverse, there seems to be a voxel shift. In looking up other freesurfer utitlites I came across xhemireg and surfreg.

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573....

Does xhemireg or surfreg call out mris_reverse, causing the same pixel shift issue???

Based on what I can find is it best to run the following: surfreg --s sub001 --t fsaverage_sym --lh --xhemi Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other hemisphere?

Thanks, Ajay

On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani <dr.ajay.kurani@gmail.com mailto:dr.ajay.kurani@gmail.com> wrote:

Hello Freesurfer Experts,

   I processed all of my brains through freesurfer 6.0 dev for
Linux and warped the surfaces to standardized space.  For a
handful of subjects I want to perform a left right flip of the
cortical thickness files (standardized space) for a group
analysis.  What is the best way to perform this in freesurfer?  I
have found a previous post referencing mris_reverse but there was
a mention of it being off by a voxel when flipped.  I wanted to
see if this is still a concern with the latest version?

Is there a better way to achieve this goal without rerunning all
of freesurfer such as a newer took, or is this the preferred method?



Thanks,
Ajay

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

hmmm, we don't have a caudate surface. How did you make it? mris_reverse just changes the sign on the x coordinate. This might not show up "properly" in freeview; it does not surprise me that it could appear to be 1 voxel off. This was not the intended use of this program. xhemireg will not help. what are you trying to do?

On 03/28/2016 06:05 PM, Ajay Kurani wrote:

Hi Doug, I attached a .png file to show an example. The Yellow outline is the right and left caudate surface. The right surface (yellow) was created by using 3dLRflip (Afni program) to symmetrically flip the volumetric ROI so that I can create the right caudate surface from scratch again. The blue outline is the same right caudate surface created when I used mris_reverse on the left hemisphere surface. As you can see the blue surface outline is not exactly symmetrical, but rather it is shifted to the left by one voxel. This was noted in some earlier posts regarding mris_reverse from 2004 as an issue (https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s... https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C[Freesurfer%5C]+R+L+flipping%22&o=newest&f=1).

I was curious to see if xhemireg or the surfreg methods alleviate this issue, or if there is another set of preferred commands to symmetrically L-R flip the brain?

Thanks, Ajay

On Mon, Mar 28, 2016 at 3:03 PM, Ajay Kurani <dr.ajay.kurani@gmail.com mailto:dr.ajay.kurani@gmail.com> wrote:

Hi Freesurfer Experts,
   In testing mris_reverse, there seems to be a voxel shift.  In
looking up other freesurfer utitlites I came across xhemireg and
surfreg.

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html

Does xhemireg or surfreg call out mris_reverse, causing the same
pixel shift issue???

Based on what I can find is it best to run the following:

surfreg --s sub001 --t fsaverage_sym --lh --xhemi
Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other hemisphere?

Thanks,

Ajay


On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani
<dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote:

    Hello Freesurfer Experts,

       I processed all of my brains through freesurfer 6.0 dev for
    Linux and warped the surfaces to standardized space.  For a
    handful of subjects I want to perform a left right flip of the
    cortical thickness files (standardized space) for a group
    analysis.  What is the best way to perform this in
    freesurfer?  I have found a previous post referencing
    mris_reverse but there was a mention of it being off by a
    voxel when flipped.  I wanted to see if this is still a
    concern with the latest version?

    Is there a better way to achieve this goal without rerunning
    all of freesurfer such as a newer took, or is this the
    preferred method?



    Thanks,
    Ajay

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

You should use xhemireg. Just changing the sign of the x coordinate will not be meaningful.

On 03/29/2016 12:49 PM, Ajay Kurani wrote:

Hi Doug, I used the caudate surface I created as an example as I was testing the command out. I do not plan to use this command for the caudate. It just happened to show the same issue as the earlier post (https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=s... https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C[Freesurfer%5C]+R+L+flipping%22&o=newest&f=1) and so I thought it would be the clearest way of showing you the issue I was referring to.

I want to flip the lh.thickness.fwhm10.fsaverage.gii files to the right hemisphere for certain subjects and I was worried about having a similar voxel shift if I used mris_reverse. I found posts using xhemireg and surfreg along with mris_reverse, and so I am trying to figure out what is the best way to flip these thickness files to the opposite hemisphere (files already warped to symmetric space)

Thanks, Ajay

On Mon, Mar 28, 2016 at 5:05 PM, Ajay Kurani <dr.ajay.kurani@gmail.com mailto:dr.ajay.kurani@gmail.com> wrote:

Hi Doug,
   I attached a .png file to show an example.  The Yellow outline
is the right and left caudate surface. The right surface (yellow)
was created by using 3dLRflip (Afni program) to symmetrically flip
the volumetric ROI so that I can create the right caudate surface
from scratch again.  The blue outline is the same right caudate
surface created when I used mris_reverse on the left hemisphere
surface.  As you can see the blue surface outline is not exactly
symmetrical, but rather it is shifted to the left by one voxel. 
This was noted in some earlier posts regarding mris_reverse from
2004 as an issue
(https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+R+L+flipping%22&o=newest&f=1
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C[Freesurfer%5C]+R+L+flipping%22&o=newest&f=1>).


I was curious to see if xhemireg or the surfreg methods alleviate
this issue, or if there is another set of preferred commands to
symmetrically L-R flip the brain?

Thanks,
Ajay

On Mon, Mar 28, 2016 at 3:03 PM, Ajay Kurani
<dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote:

    Hi Freesurfer Experts,
       In testing mris_reverse, there seems to be a voxel shift. 
    In looking up other freesurfer utitlites I came across
    xhemireg and surfreg.

    https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html

    Does xhemireg or surfreg call out mris_reverse, causing the
    same pixel shift issue???

    Based on what I can find is it best to run the following:

    surfreg --s sub001 --t fsaverage_sym --lh --xhemi
    Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other hemisphere?

    Thanks,

    Ajay


    On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani
    <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>>
    wrote:

        Hello Freesurfer Experts,

           I processed all of my brains through freesurfer 6.0 dev
        for Linux and warped the surfaces to standardized space. 
        For a handful of subjects I want to perform a left right
        flip of the cortical thickness files (standardized space)
        for a group analysis.  What is the best way to perform
        this in freesurfer?  I have found a previous post
        referencing mris_reverse but there was a mention of it
        being off by a voxel when flipped.  I wanted to see if
        this is still a concern with the latest version?

        Is there a better way to achieve this goal without
        rerunning all of freesurfer such as a newer took, or is
        this the preferred method?



        Thanks,
        Ajay

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer