subject:"Re\: \[Freesurfer\] Shifted surface after gyrification index is calculated"

Re: [Freesurfer] Shifted surface after gyrification index is calculated

2015-12-10 Thread Bruce Fischl

and how do you determine they are shifted? In freeview? The surface 
geometry/position should be preserved in the smoothing but appears to not 
to be. Perhaps Marie can comment? Or you can try mris_copy_header to see if 
that does the trick

cheers
Bruce

On Thu, 10 Dec 2015, 
Chris Holdgraf wrote:

Hey Bruce - thus far I have used pretty default parameters. I first ran
recon-all on each subject, then simply ran `recon-all -s s_name -localGI`. 
Here are the transforms for the original vs. inflated surface

On lh.pial:
talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.752;
-0.032   1.064   0.063  -15.999;
 0.015  -0.008   1.170   1.733;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.519;
 0.028   0.939  -0.051   14.976;
-0.012   0.007   0.854  -1.320;
 0.000   0.000   0.000   1.000;
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 0.5078,  2.0802, 23.0431)

On lh.pial-outer-smoothed:

talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.011;
 0.028   0.939  -0.051   17.057;
-0.012   0.007   0.854   21.723;
 0.000   0.000   0.000   1.000;
volume geometry info is either not contained or not valid.

---

I highlight that last bit because maybe it's important? Looks like some
information goes missing in there...

Chris

On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl 
wrote:
  Hi Chris

  how do you smooth the surface? Are you sure that you retain the
  surface
  header information? Try looking at the header with mris_info
  before and
  after smoothing

  cheers
  Bruce
  On Thu, 10 Dec 2015, Chris Holdgraf wrote:

  > Hey Freesurfer folks - I'm looking into using Freesurfer for
  doing electrode
  > reconstruction / co-registration in electrocorticography.
  We're making good
  > progress on figuring out recon-all for surfaces and doing
  co-registration to
  > CTs. However, I think I've encountered a strange bug.
  > I'm trying to create a smoothed pial surface so that I project
  electrodes
  > onto this surface. The code seems to run correctly, however,
  the smoothed
  > surface looks translated relative to the original pial surface
  that it was
  > created from.
  >
  > For example, see this issue I opened on github:
  >
  > https://github.com/aestrivex/gselu/issues/7
  >
  > Anyone have an idea why this is happening? I'm not sure why
  the pial surface
  > would be correct, while the smoothed surface would be shifted.
  >
  > Chris
  >
  >
  > --
  > _
  >
  > PhD Candidate in Neuroscience | UC Berkeley
  > Editor and Web Director | Berkeley Science Review
  > _
  >
  >
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Re: [Freesurfer] Shifted surface after gyrification index is calculated

2015-12-10 Thread Chris Holdgraf

Yep - sorry, here's a pic:
https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9e89-11e5-8485-dc97c8ca2ca7.png

You can see the smoothed version is shifted lower.

I couldn't find mris_copy_header on my path. Is it only included in the
beta version? I'm running 5.3. Could try beta as well, just not sure how
stable it is...

On Thu, Dec 10, 2015 at 12:38 PM, Bruce Fischl 
wrote:

> and how do you determine they are shifted? In freeview? The surface
> geometry/position should be preserved in the smoothing but appears to not
> to be. Perhaps Marie can comment? Or you can try mris_copy_header to see if
> that does the trick
>
>
> cheers
> Bruce
>
>
> On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>
> Hey Bruce - thus far I have used pretty default parameters. I first ran
>> recon-all on each subject, then simply ran `recon-all -s s_name
>> -localGI`.
>> Here are the transforms for the original vs. inflated surface
>>
>> On lh.pial:
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.752;
>> -0.032   1.064   0.063  -15.999;
>>  0.015  -0.008   1.170   1.733;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.519;
>>  0.028   0.939  -0.051   14.976;
>> -0.012   0.007   0.854  -1.320;
>>  0.000   0.000   0.000   1.000;
>> volume geometry:
>> extent  : (256, 256, 256)
>> voxel   : ( 1.,  1.,  1.)
>> x_(ras) : (-1.,  0.,  0.)
>> y_(ras) : ( 0.,  0., -1.)
>> z_(ras) : ( 0.,  1.,  0.)
>> c_(ras) : ( 0.5078,  2.0802, 23.0431)
>>
>>
>> On lh.pial-outer-smoothed:
>>
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.011;
>>  0.028   0.939  -0.051   17.057;
>> -0.012   0.007   0.854   21.723;
>>  0.000   0.000   0.000   1.000;
>> volume geometry info is either not contained or not valid.
>>
>> ---
>>
>> I highlight that last bit because maybe it's important? Looks like some
>> information goes missing in there...
>>
>> Chris
>>
>>
>>
>> On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Chris
>>
>>   how do you smooth the surface? Are you sure that you retain the
>>   surface
>>   header information? Try looking at the header with mris_info
>>   before and
>>   after smoothing
>>
>>   cheers
>>   Bruce
>>   On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>>
>>   > Hey Freesurfer folks - I'm looking into using Freesurfer for
>>   doing electrode
>>   > reconstruction / co-registration in electrocorticography.
>>   We're making good
>>   > progress on figuring out recon-all for surfaces and doing
>>   co-registration to
>>   > CTs. However, I think I've encountered a strange bug.
>>   > I'm trying to create a smoothed pial surface so that I project
>>   electrodes
>>   > onto this surface. The code seems to run correctly, however,
>>   the smoothed
>>   > surface looks translated relative to the original pial surface
>>   that it was
>>   > created from.
>>   >
>>   > For example, see this issue I opened on github:
>>   >
>>   > https://github.com/aestrivex/gselu/issues/7
>>   >
>>   > Anyone have an idea why this is happening? I'm not sure why
>>   the pial surface
>>   > would be correct, while the smoothed surface would be shifted.
>>   >
>>   > Chris
>>   >
>>   >
>>   > --
>>   > _
>>   >
>>   > PhD Candidate in Neuroscience | UC Berkeley
>>   > Editor and Web Director | Berkeley Science Review
>>   > _
>>   >
>>   >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> _
>>
>> PhD Candidate in Neuroscience | UC Berkeley
>> Editor and Web

Re: [Freesurfer] Shifted surface after gyrification index is calculated

2015-12-10 Thread Bruce Fischl

what hardware are you running on? We can send you a version of 
mris_copy_header. Or you can can send me the two surfaces (before and 
after smoothing) and I can see if it fixes the problem

cheers
Bruce
On Thu, 10 Dec 2015, 
Chris Holdgraf wrote:

Yep - sorry, here's apic: 
https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9
e89-11e5-8485-dc97c8ca2ca7.png
You can see the smoothed version is shifted lower. 

I couldn't find mris_copy_header on my path. Is it only included in the beta
version? I'm running 5.3. Could try beta as well, just not sure how stable
it is...

On Thu, Dec 10, 2015 at 12:38 PM, Bruce Fischl 
wrote:
  and how do you determine they are shifted? In freeview? The
  surface geometry/position should be preserved in the smoothing
  but appears to not to be. Perhaps Marie can comment? Or you can
  try mris_copy_header to see if that does the trick

  cheers
  Bruce

  On Thu, 10 Dec 2015, Chris Holdgraf wrote:

Hey Bruce - thus far I have used pretty default
parameters. I first ran
recon-all on each subject, then simply ran
`recon-all -s s_name -localGI`. 
Here are the transforms for the original vs.
inflated surface

On lh.pial:
talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.752;
-0.032   1.064   0.063  -15.999;
 0.015  -0.008   1.170   1.733;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.519;
 0.028   0.939  -0.051   14.976;
-0.012   0.007   0.854  -1.320;
 0.000   0.000   0.000   1.000;
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 0.5078,  2.0802, 23.0431)

On lh.pial-outer-smoothed:

talairch.xfm: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS: 
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS: 
 0.906  -0.013   0.002  -4.011;
 0.028   0.939  -0.051   17.057;
-0.012   0.007   0.854   21.723;
 0.000   0.000   0.000   1.000;
volume geometry info is either not contained or not
valid.

---

I highlight that last bit because maybe it's
important? Looks like some
information goes missing in there...

Chris

On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl

wrote:
      Hi Chris

      how do you smooth the surface? Are you sure
that you retain the
      surface
      header information? Try looking at the header
with mris_info
      before and
      after smoothing

      cheers
      Bruce
      On Thu, 10 Dec 2015, Chris Holdgraf wrote:

      > Hey Freesurfer folks - I'm looking into
using Freesurfer for
      doing electrode
      > reconstruction / co-registration in
electrocorticography.
      We're making good
      > progress on figuring out recon-all for
surfaces and doing
      co-registration to
      > CTs. However, I think I've encountered a
strange bug.
      > I'm trying to create a smoothed pial surface
so that I project
      electrodes
      > onto this surface. The code seems to run
correctly, however,
      the smoothed
      > surface looks translated relative to the
original pial surface
      that it was
      > created from.
      >
      > For example, see this issue I opened on
github:
      >
      > https://github.com/aestrivex/gselu/issues/7
      >
      > Anyone have an idea why this is happening?
I'm not sure why

Re: [Freesurfer] Shifted surface after gyrification index is calculated

2015-12-10 Thread Chris Holdgraf

It's a cluster running Linux CentOS 64-bit. If it's as simple as getting
the file and adding it to my path I'm happy to give it a try...

Chris

On Thu, Dec 10, 2015 at 1:47 PM, Bruce Fischl 
wrote:

> what hardware are you running on? We can send you a version of
> mris_copy_header. Or you can can send me the two surfaces (before and after
> smoothing) and I can see if it fixes the problem
>
> cheers
> Bruce
> On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>
> Yep - sorry, here's apic:
>> https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9
>> e89-11e5-8485-dc97c8ca2ca7.png
>> You can see the smoothed version is shifted lower.
>>
>> I couldn't find mris_copy_header on my path. Is it only included in the
>> beta
>> version? I'm running 5.3. Could try beta as well, just not sure how stable
>> it is...
>>
>> On Thu, Dec 10, 2015 at 12:38 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   and how do you determine they are shifted? In freeview? The
>>   surface geometry/position should be preserved in the smoothing
>>   but appears to not to be. Perhaps Marie can comment? Or you can
>>   try mris_copy_header to see if that does the trick
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>>
>> Hey Bruce - thus far I have used pretty default
>> parameters. I first ran
>> recon-all on each subject, then simply ran
>> `recon-all -s s_name -localGI`.
>> Here are the transforms for the original vs.
>> inflated surface
>>
>> On lh.pial:
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.752;
>> -0.032   1.064   0.063  -15.999;
>>  0.015  -0.008   1.170   1.733;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.519;
>>  0.028   0.939  -0.051   14.976;
>> -0.012   0.007   0.854  -1.320;
>>  0.000   0.000   0.000   1.000;
>> volume geometry:
>> extent  : (256, 256, 256)
>> voxel   : ( 1.,  1.,  1.)
>> x_(ras) : (-1.,  0.,  0.)
>> y_(ras) : ( 0.,  0., -1.)
>> z_(ras) : ( 0.,  1.,  0.)
>> c_(ras) : ( 0.5078,  2.0802, 23.0431)
>>
>>
>> On lh.pial-outer-smoothed:
>>
>> talairch.xfm:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> surfaceRAS to talaraiched surfaceRAS:
>>  1.103   0.015  -0.002   4.202;
>> -0.032   1.064   0.063  -19.651;
>>  0.015  -0.008   1.170  -25.227;
>>  0.000   0.000   0.000   1.000;
>> talairached surfaceRAS to surfaceRAS:
>>  0.906  -0.013   0.002  -4.011;
>>  0.028   0.939  -0.051   17.057;
>> -0.012   0.007   0.854   21.723;
>>  0.000   0.000   0.000   1.000;
>> volume geometry info is either not contained or not
>> valid.
>>
>> ---
>>
>> I highlight that last bit because maybe it's
>> important? Looks like some
>> information goes missing in there...
>>
>> Chris
>>
>>
>>
>> On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Chris
>>
>>   how do you smooth the surface? Are you sure
>> that you retain the
>>   surface
>>   header information? Try looking at the header
>> with mris_info
>>   before and
>>   after smoothing
>>
>>   cheers
>>   Bruce
>>   On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>>
>>   > Hey Freesurfer folks - I'm looking into
>> using Freesurfer for
>>   doing electrode
>>   > reconstruction / co-registration in
>> electrocorticography.
>>   We're making good
>>   > progress on figuring out recon-all for
>> surfaces and doing
>>   co-registration to
>>   > CTs. However, I think I've encountered a
>> strange bug.
>>   > I'm trying to create a smoothed pial surface
>> so that I project
>>   electrodes
>>   > onto this

Re: [Freesurfer] Shifted surface after gyrification index is calculated

2015-12-10 Thread Bruce Fischl

Hi Chris

how do you smooth the surface? Are you sure that you retain the surface 
header information? Try looking at the header with mris_info before and 
after smoothing

cheers
Bruce
On Thu, 10 Dec 2015, Chris Holdgraf wrote:

> Hey Freesurfer folks - I'm looking into using Freesurfer for doing electrode
> reconstruction / co-registration in electrocorticography. We're making good
> progress on figuring out recon-all for surfaces and doing co-registration to
> CTs. However, I think I've encountered a strange bug.
> I'm trying to create a smoothed pial surface so that I project electrodes
> onto this surface. The code seems to run correctly, however, the smoothed
> surface looks translated relative to the original pial surface that it was
> created from.
> 
> For example, see this issue I opened on github:
> 
> https://github.com/aestrivex/gselu/issues/7
> 
> Anyone have an idea why this is happening? I'm not sure why the pial surface
> would be correct, while the smoothed surface would be shifted.
> 
> Chris
> 
> 
> --
> _
> 
> PhD Candidate in Neuroscience | UC Berkeley
> Editor and Web Director | Berkeley Science Review
> _
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.

Re: [Freesurfer] Shifted surface after gyrification index is calculated

2015-12-10 Thread Chris Holdgraf

Hey Bruce - thus far I have used pretty default parameters. I first ran
recon-all on each subject, then simply ran `recon-all -s s_name -localGI`.

Here are the transforms for the original vs. inflated surface

On lh.pial:
talairch.xfm:
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS:
 1.103   0.015  -0.002   4.752;
-0.032   1.064   0.063  -15.999;
 0.015  -0.008   1.170   1.733;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS:
 0.906  -0.013   0.002  -4.519;
 0.028   0.939  -0.051   14.976;
-0.012   0.007   0.854  -1.320;
 0.000   0.000   0.000   1.000;
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 0.5078,  2.0802, 23.0431)


On lh.pial-outer-smoothed:

talairch.xfm:
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS:
 1.103   0.015  -0.002   4.202;
-0.032   1.064   0.063  -19.651;
 0.015  -0.008   1.170  -25.227;
 0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS:
 0.906  -0.013   0.002  -4.011;
 0.028   0.939  -0.051   17.057;
-0.012   0.007   0.854   21.723;
 0.000   0.000   0.000   1.000;
*volume geometry info is either not contained or not valid.*

---

I highlight that last bit because maybe it's important? Looks like some
information goes missing in there...

Chris



On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl 
wrote:

> Hi Chris
>
> how do you smooth the surface? Are you sure that you retain the surface
> header information? Try looking at the header with mris_info before and
> after smoothing
>
> cheers
> Bruce
> On Thu, 10 Dec 2015, Chris Holdgraf wrote:
>
> > Hey Freesurfer folks - I'm looking into using Freesurfer for doing
> electrode
> > reconstruction / co-registration in electrocorticography. We're making
> good
> > progress on figuring out recon-all for surfaces and doing
> co-registration to
> > CTs. However, I think I've encountered a strange bug.
> > I'm trying to create a smoothed pial surface so that I project electrodes
> > onto this surface. The code seems to run correctly, however, the smoothed
> > surface looks translated relative to the original pial surface that it
> was
> > created from.
> >
> > For example, see this issue I opened on github:
> >
> > https://github.com/aestrivex/gselu/issues/7
> >
> > Anyone have an idea why this is happening? I'm not sure why the pial
> surface
> > would be correct, while the smoothed surface would be shifted.
> >
> > Chris
> >
> >
> > --
> > _
> >
> > PhD Candidate in Neuroscience | UC Berkeley
> > Editor and Web Director | Berkeley Science Review
> > _
> >
> >
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-- 
_

PhD Candidate in Neuroscience | UC Berkeley 
Editor and Web Director | Berkeley Science Review

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Shifted surface after gyrification index is calculated

Re: [Freesurfer] Shifted surface after gyrification index is calculated

Re: [Freesurfer] Shifted surface after gyrification index is calculated

Re: [Freesurfer] Shifted surface after gyrification index is calculated

Re: [Freesurfer] Shifted surface after gyrification index is calculated

Re: [Freesurfer] Shifted surface after gyrification index is calculated

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