Re: [Freesurfer] reposition surface for pial surface

[miracle ozzoude]

Hello Antonin,
Apologies, I forgot to send them. This is the email and the vertex
coordinates. For vertex, it shows N/A hence, not sure what value i need to
enter in the vertex section of edit coordinates in the reposition surface
tool. Thank you
Best,
Paul

On Tue, Jan 10, 2017 at 4:54 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I cannot see your attachment since I am only getting mail digest (without
> attachments) and the mail archive does not store attachments.
>
> I do not know for which option of surface reposition your question refers
> to. But, I hope when you play with the tool, you will figure out, as I did.
>
> Also, what do you mean, what step you should start?
> In case of "volume based" reposition, when you click on "apply", you
> internally invoke customized mris_make_surfaces code on the surface you
> want to modify. The run takes several seconds and when it is finished, you
> will see the result of reposition. Then you inspect the surface and when
> you are satisfied, you save the modified surface (by the proper name, i.e.
> overwriting the original surface, you can save it by different name before
> using this tool to be able to get back). Then you should rerun remaining
> steps of recon-all, which for example in case of V6beta after repositioning
> pial surface means running
>
> recon-all -s my_subject -cortribbon -parcstats -cortparc2 -parcstats2
> -cortparc3 -pctsurfcon -hyporelabel -aparc2aseg -apas2aseg -segstats
> -wmparc -balabels
>
> Antonin
>
> Thank you very much Antonin. I do appreciate it. Do I need to insert a
> vertex number or just the coordinates? Because when i clicked on the
> surface outside the pial (see screenshot) the vertex = N/A ( see
> screenshot). ALso, what step of recon-all should i start? (autorecon-2 or
> autorecon3)?
> Best,
> Paul
>
> On Tue, Jan 10, 2017 at 3:52 PM, Antonin Skoch  wrote:
>
> > Dear Paul,
> >
> > I could chime in with my current limited experiences with this tool (using
> > V6beta version of freeview). Maybe they could be helpful for you.
> >
> > Most straigthforward is using "edit coordinate":
> >
> > Select the surface you want to edit.
> > Select tools-reposition surface - edit coordinate.
> > With shift + left mouse button click on the surface to pick particular
> > vertex.
> > Manually enter new coordinates of the vertex.
> > Save surface to store edits.
> > This is prohibitively time consuming in case of large error, so it is
> > usable only in case of small errors.
> >
> > However, you can try to use combination of "edit coordinate" and "smooth".
> > By smoothing you can nudge some area of adjacent vertices to desired
> > position.
> >
> > I was partially successful  also with using
> > reposition surface - volume based - coordinate:
> > With shift + left mouse button select particular vertex
> > In "volumes", load volume according to what you want to reposition the
> > surface.
> > With shift + ctrl + left mouse button click at the coordinate you want to
> > reposition the surface to.
> > Save surface to store edits.
> >
> > Regarding the parameters:
> > The "size" textfield determine the extent of the vertex neighbourhood
> > which would be repositioned. Do not use too large value since then the
> > behaviour is unpredictable, in my case the maximal resonable value is
> > around 5.
> > I am not sure about "sigma" parameter, maybe it has to do something with
> > the smoothing (of the underlying volume?),  however in my case altering
> > this parameter did not change behaviour much.
> > Also, the "gradient direction" in my case did not change much, in many
> > cases it produced identical result regardless of the gradient direction
> > selected.
> >
> > In most cases, I was not satisfied with the result of the reposition, the
> > particular vertex moved to desired position, however position of adjacent
> > vertices did not make sense, mostly the surface got very jagged and
> > irregular, with worsening of the position in areas where the position was
> > good previously, etc. However, subsequent using of "smooth" usually
> > improved the shape and after many iterations I finally arrived to desired
> > shape of surface.
> >
> > I also tried to study the relevant source code to learn the behavior of
> > this tool and the significance of the parameters, but it is very
> > complicated to me to comprehend (so far..).
> >
> > Note that after using this tool you should rerun remaining code of
> > recon-all
> >
> > ReconAllDevTable
> > https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
> > (for development version) would tell you which particular steps should be
> > rerun.
> > Please note that in case of  rerun of recon-all from start you will lose
> > all modifications of surfaces you achieved using this tool.
> >
> > And, particularly, many surface errors can be corrected by editing the
> > volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control
> > points to the white matter.
> > Large 

Re: [Freesurfer] reposition surface for pial surface

[Antonin Skoch]

Dear Paul,

I cannot see your attachment since I am only getting mail digest (without 
attachments) and the mail archive does not store attachments.

I do not know for which option of surface reposition your question refers to. 
But, I hope when you play with the tool, you will figure out, as I did.

Also, what do you mean, what step you should start?
In case of "volume based" reposition, when you click on "apply", you internally 
invoke customized mris_make_surfaces code on the surface you want to modify. 
The run takes several seconds and when it is finished, you will see the result 
of reposition. Then you inspect the surface and when you are satisfied, you 
save the modified surface (by the proper name, i.e. overwriting the original 
surface, you can save it by different name before using this tool to be able to 
get back). Then you should rerun remaining steps of recon-all, which for 
example in case of V6beta after repositioning pial surface means running

recon-all -s my_subject -cortribbon -parcstats -cortparc2 -parcstats2 
-cortparc3 -pctsurfcon -hyporelabel -aparc2aseg -apas2aseg -segstats -wmparc 
-balabels

Antonin

Thank you very much Antonin. I do appreciate it. Do I need to insert a
vertex number or just the coordinates? Because when i clicked on the
surface outside the pial (see screenshot) the vertex = N/A ( see
screenshot). ALso, what step of recon-all should i start? (autorecon-2 or
autorecon3)?
Best,
PaulOn Tue, Jan 10, 2017 at 3:52 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I could chime in with my current limited experiences with this tool (using
> V6beta version of freeview). Maybe they could be helpful for you.
>
> Most straigthforward is using "edit coordinate":
>
> Select the surface you want to edit.
> Select tools-reposition surface - edit coordinate.
> With shift + left mouse button click on the surface to pick particular
> vertex.
> Manually enter new coordinates of the vertex.
> Save surface to store edits.
> This is prohibitively time consuming in case of large error, so it is
> usable only in case of small errors.
>
> However, you can try to use combination of "edit coordinate" and "smooth".
> By smoothing you can nudge some area of adjacent vertices to desired
> position.
>
> I was partially successful  also with using
> reposition surface - volume based - coordinate:
> With shift + left mouse button select particular vertex
> In "volumes", load volume according to what you want to reposition the
> surface.
> With shift + ctrl + left mouse button click at the coordinate you want to
> reposition the surface to.
> Save surface to store edits.
>
> Regarding the parameters:
> The "size" textfield determine the extent of the vertex neighbourhood
> which would be repositioned. Do not use too large value since then the
> behaviour is unpredictable, in my case the maximal resonable value is
> around 5.
> I am not sure about "sigma" parameter, maybe it has to do something with
> the smoothing (of the underlying volume?),  however in my case altering
> this parameter did not change behaviour much.
> Also, the "gradient direction" in my case did not change much, in many
> cases it produced identical result regardless of the gradient direction
> selected.
>
> In most cases, I was not satisfied with the result of the reposition, the
> particular vertex moved to desired position, however position of adjacent
> vertices did not make sense, mostly the surface got very jagged and
> irregular, with worsening of the position in areas where the position was
> good previously, etc. However, subsequent using of "smooth" usually
> improved the shape and after many iterations I finally arrived to desired
> shape of surface.
>
> I also tried to study the relevant source code to learn the behavior of
> this tool and the significance of the parameters, but it is very
> complicated to me to comprehend (so far..).
>
> Note that after using this tool you should rerun remaining code of
> recon-all
>
> ReconAllDevTable
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
> (for development version) would tell you which particular steps should be
> rerun.
> Please note that in case of  rerun of recon-all from start you will lose
> all modifications of surfaces you achieved using this tool.
>
> And, particularly, many surface errors can be corrected by editing the
> volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control
> points to the white matter.
> Large errors of ?h.white (and subsequently ?h.pial) can be caused of
> wrongly corrected topological defect (which you can diagnose by inspecting
> ?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz
> would help to correct the issue.
> I also came across the error when ?h.white was cut off the particular
> gyrus near midline, which was caused by erroneous labeling of cortex in
> aseg.mgz (gyrus was attributed to contralateral hemisphere). Editing of
> aseg.mgz by assignment of the gyrus to correct 

Re: [Freesurfer] reposition surface for pial surface

[miracle ozzoude]

Thank you very much Antonin. I do appreciate it. Do I need to insert a
vertex number or just the coordinates? Because when i clicked on the
surface outside the pial (see screenshot) the vertex = N/A ( see
screenshot). ALso, what step of recon-all should i start? (autorecon-2 or
autorecon3)?
Best,
Paul

On Tue, Jan 10, 2017 at 3:52 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I could chime in with my current limited experiences with this tool (using
> V6beta version of freeview). Maybe they could be helpful for you.
>
> Most straigthforward is using "edit coordinate":
>
> Select the surface you want to edit.
> Select tools-reposition surface - edit coordinate.
> With shift + left mouse button click on the surface to pick particular
> vertex.
> Manually enter new coordinates of the vertex.
> Save surface to store edits.
> This is prohibitively time consuming in case of large error, so it is
> usable only in case of small errors.
>
> However, you can try to use combination of "edit coordinate" and "smooth".
> By smoothing you can nudge some area of adjacent vertices to desired
> position.
>
> I was partially successful  also with using
> reposition surface - volume based - coordinate:
> With shift + left mouse button select particular vertex
> In "volumes", load volume according to what you want to reposition the
> surface.
> With shift + ctrl + left mouse button click at the coordinate you want to
> reposition the surface to.
> Save surface to store edits.
>
> Regarding the parameters:
> The "size" textfield determine the extent of the vertex neighbourhood
> which would be repositioned. Do not use too large value since then the
> behaviour is unpredictable, in my case the maximal resonable value is
> around 5.
> I am not sure about "sigma" parameter, maybe it has to do something with
> the smoothing (of the underlying volume?),  however in my case altering
> this parameter did not change behaviour much.
> Also, the "gradient direction" in my case did not change much, in many
> cases it produced identical result regardless of the gradient direction
> selected.
>
> In most cases, I was not satisfied with the result of the reposition, the
> particular vertex moved to desired position, however position of adjacent
> vertices did not make sense, mostly the surface got very jagged and
> irregular, with worsening of the position in areas where the position was
> good previously, etc. However, subsequent using of "smooth" usually
> improved the shape and after many iterations I finally arrived to desired
> shape of surface.
>
> I also tried to study the relevant source code to learn the behavior of
> this tool and the significance of the parameters, but it is very
> complicated to me to comprehend (so far..).
>
> Note that after using this tool you should rerun remaining code of
> recon-all
>
> ReconAllDevTable
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
> (for development version) would tell you which particular steps should be
> rerun.
> Please note that in case of  rerun of recon-all from start you will lose
> all modifications of surfaces you achieved using this tool.
>
> And, particularly, many surface errors can be corrected by editing the
> volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control
> points to the white matter.
> Large errors of ?h.white (and subsequently ?h.pial) can be caused of
> wrongly corrected topological defect (which you can diagnose by inspecting
> ?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz
> would help to correct the issue.
> I also came across the error when ?h.white was cut off the particular
> gyrus near midline, which was caused by erroneous labeling of cortex in
> aseg.mgz (gyrus was attributed to contralateral hemisphere). Editing of
> aseg.mgz by assignment of the gyrus to correct hemisphere corrected the
> error.
>
> Also, altering several of global parameters of mris_make_surfaces, as
> listed for example here
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html
>
> could help you to get satisfactory results (however, the altering of these
> parameters should be done in my opinion for all subjects in the study to
> avoid bias).
>
> Regards,
>
> Antonin
>
> Thanks bruce for your response. Since there is no documentation, how can i
> use it because I seen trends on the forum where it was suggested to use
> reposition surface ( 
> e.g.https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html).
> Use = directions and parameters to input. Thanks
> Best,
> Paul
>
> On Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl 
> wrote:
>
> > Hi Paul
> >
> > sorry, this is something that Ruopeng put together for me to mess around
> > with - there isn't any documentation
> >
> > cheers
> > Bruce
> >
> > On Tue, 10 Jan 2017, miracle ozzoude wrote:
> >
> > Hello Freesurfer, I would like to learn how to use the reposition surface
> >> tool in freeview. 

[Freesurfer] reposition surface for pial surface

[Antonin Skoch]

Dear Paul,

I could chime in with my current limited experiences with this tool (using 
V6beta version of freeview). Maybe they could be helpful for you.

Most straigthforward is using "edit coordinate":

Select the surface you want to edit.
Select tools-reposition surface - edit coordinate.
With shift + left mouse button click on the surface to pick particular vertex.
Manually enter new coordinates of the vertex.
Save surface to store edits.
This is prohibitively time consuming in case of large error, so it is usable 
only in case of small errors.

However, you can try to use combination of "edit coordinate" and "smooth". By 
smoothing you can nudge some area of adjacent vertices to desired position. 

I was partially successful  also with using 
reposition surface - volume based - coordinate:
With shift + left mouse button select particular vertex
In "volumes", load volume according to what you want to reposition the surface. 
With shift + ctrl + left mouse button click at the coordinate you want to 
reposition the surface to.
Save surface to store edits.

Regarding the parameters:
The "size" textfield determine the extent of the vertex neighbourhood which 
would be repositioned. Do not use too large value since then the behaviour is 
unpredictable, in my case the maximal resonable value is around 5.
I am not sure about "sigma" parameter, maybe it has to do something with the 
smoothing (of the underlying volume?),  however in my case altering this 
parameter did not change behaviour much.
Also, the "gradient direction" in my case did not change much, in many cases it 
produced identical result regardless of the gradient direction selected.

In most cases, I was not satisfied with the result of the reposition, the 
particular vertex moved to desired position, however position of adjacent 
vertices did not make sense, mostly the surface got very jagged and irregular, 
with worsening of the position in areas where the position was good previously, 
etc. However, subsequent using of "smooth" usually improved the shape and after 
many iterations I finally arrived to desired shape of surface.

I also tried to study the relevant source code to learn the behavior of this 
tool and the significance of the parameters, but it is very complicated to me 
to comprehend (so far..).

Note that after using this tool you should rerun remaining code of recon-all

ReconAllDevTable
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
(for development version) would tell you which particular steps should be rerun.
Please  note that in case of  rerun of recon-all from start you will lose all  
modifications of surfaces you achieved using this tool.

And, particularly, many surface errors can be corrected by editing the volume 
(particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control points to the 
white matter.
Large errors of ?h.white (and subsequently ?h.pial) can be caused of wrongly 
corrected topological defect (which you can diagnose by inspecting 
?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz would 
help to correct the issue.
I also came across the error when ?h.white was cut off the particular gyrus 
near midline, which was caused by erroneous labeling of cortex in aseg.mgz 
(gyrus was attributed to contralateral hemisphere). Editing of aseg.mgz by 
assignment of the gyrus to correct hemisphere corrected the error.

Also, altering several of global parameters of mris_make_surfaces, as listed 
for example here

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html

could help you to get satisfactory results (however, the altering of these 
parameters should be done in my opinion for all subjects in the study to avoid 
bias).

Regards,

Antonin
Thanks bruce for your response. Since there is no documentation, how can i
use it because I seen trends on the forum where it was suggested to use
reposition surface ( e.g.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html).
Use = directions and parameters to input. Thanks
Best,
PaulOn Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> sorry, this is something that Ruopeng put together for me to mess around
> with - there isn't any documentation
>
> cheers
> Bruce
>
> On Tue, 10 Jan 2017, miracle ozzoude wrote:
>
> Hello Freesurfer, I would like to learn how to use the reposition surface
>> tool in freeview. Specifically, what parameters to enter in the gui (see
>> screenshots). Is there any documentation on how to use it if not, can
>> someone with experience work me through it. Thank you.
>> best,
>> Paul

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Re: [Freesurfer] reposition surface for pial surface

[miracle ozzoude]

Thanks bruce for your response. Since there is no documentation, how can i
use it because I seen trends on the forum where it was suggested to use
reposition surface ( e.g.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html).
Use = directions and parameters to input. Thanks
Best,
Paul

On Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> sorry, this is something that Ruopeng put together for me to mess around
> with - there isn't any documentation
>
> cheers
> Bruce
>
> On Tue, 10 Jan 2017, miracle ozzoude wrote:
>
> Hello Freesurfer, I would like to learn how to use the reposition surface
>> tool in freeview. Specifically, what parameters to enter in the gui (see
>> screenshots). Is there any documentation on how to use it if not, can
>> someone with experience work me through it. Thank you.
>> best,
>> Paul
>>
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] reposition surface for pial surface

[Bruce Fischl]

Hi Paul

sorry, this is something that Ruopeng put together for me to mess around 
with - there isn't any documentation


cheers
Bruce
On Tue, 10 Jan 2017, miracle ozzoude 
wrote:



Hello Freesurfer, I would like to learn how to use the reposition surface
tool in freeview. Specifically, what parameters to enter in the gui (see
screenshots). Is there any documentation on how to use it if not, can
someone with experience work me through it. Thank you. 
best, 
Paul


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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] reposition surface for pial surface

[miracle ozzoude]

Hello Freesurfer,
I would like to learn how to use the reposition surface tool in freeview.
Specifically, what parameters to enter in the gui (see screenshots). Is
there any documentation on how to use it if not, can someone with
experience work me through it. Thank you.
best,
Paul
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Reposition Surface

[Derin J Cobia]

Just a question about the Tools -- Reposition Surface... feature in Freeview. 
Is that up and running? Is there any accompanying documentation? Thanks.

-Derin



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contains patient information, please contact the Partners Compliance HelpLine at
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