lh.orig.nofix vs. lh.white

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David Romano

4 Sep 2013 4 Sep '13

7:07 p.m.

Hi everyone,

I've been trying to go through the various steps described on the page:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

and I'm trying to understand part of the -autorecon2 section, and in particular,

1) how the lh.orig.nofix file that is produced by the end of the -tessellate subsection is different from the the lh.white file that is produced by the -white subsection, and

2) whether the area and curvature files produced by the command

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Douglas N Greve

4 Sep 4 Sep

7:10 p.m.

lh.orig.nofix is the original tesselation without anything done to it. To get to lh.white, the defects are automatically corrected to create lh.orig. lh.orig is then refined with smoothness and intensity constraints to produce lh.white doug

On 09/04/2013 07:07 PM, David Romano wrote:

...

Hi everyone,

I've been trying to go through the various steps described on the page:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

and I'm trying to understand part of the -autorecon2 section, and in particular,

how the lh.orig.nofix file that is produced by the end of the

-tessellate subsection is different from the the lh.white file that is produced by the -white subsection, and

whether the area and curvature files produced by the command

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

David Romano

7:56 p.m.

Thanks, Doug; this helps me to formulate my second question better, which is:

2) Assuming that no change in intensity is necessary, would the files lh.white, lh.area, and lh.curv produced by the mri_make_surfaces command (in the -white subsection of the -autorecon2 section) be the same as the files produced by the command

mri_smooth lh.orig lh.white?

(Note that I dropped the flag -nw, so this will produce lh.area and lh.curv files.)

Thanks again, David

On Wed, Sep 4, 2013 at 4:10 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

...

lh.orig.nofix is the original tesselation without anything done to it. To get to lh.white, the defects are automatically corrected to create lh.orig. lh.orig is then refined with smoothness and intensity constraints to produce lh.white doug

On 09/04/2013 07:07 PM, David Romano wrote:

...
Hi everyone,

I've been trying to go through the various steps described on the page:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

and I'm trying to understand part of the -autorecon2 section, and in particular,

how the lh.orig.nofix file that is produced by the end of the

-tessellate subsection is different from the the lh.white file that is produced by the -white subsection, and

whether the area and curvature files produced by the command

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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.

Bruce Fischl

8:59 p.m.

no, the smoothing is done irrespective of the intensity volume (in mris_smooth). The smoothness constraints in mris_make_surfaces are more sophisticated (they assume that the surfaces are well-fit by quadratic patches, not planes) and also move the surface to lie at large intensity gradients

On Wed, 4 Sep 2013, David Romano wrote:

...

Thanks, Doug; this helps me to formulate my second question better, which is:

Assuming that no change in intensity is necessary, would the files

lh.white, lh.area, and lh.curv produced by the mri_make_surfaces command (in the -white subsection of the -autorecon2 section) be the same as the files produced by the command

mri_smooth lh.orig lh.white?

(Note that I dropped the flag -nw, so this will produce lh.area and lh.curv files.)

Thanks again, David

On Wed, Sep 4, 2013 at 4:10 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
  lh.orig.nofix is the original tesselation without anything done
  to it.
  To get to lh.white, the defects are automatically corrected to
  create
  lh.orig. lh.orig is then refined with smoothness and intensity
  constraints to produce lh.white
  doug


  On 09/04/2013 07:07 PM, David Romano wrote:
  > Hi everyone,
  >
  > I've been trying to go through the various steps described on
  the page:
  >
  > http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
  >
  > and I'm trying to understand part of the -autorecon2 section,
  and in
  > particular,
  >
  > 1) how the lh.orig.nofix file that is produced by the end of
  the
  > -tessellate subsection is different from the the lh.white file
  that is
  > produced by the -white subsection, and
  >
  > 2) whether the area and curvature files produced by the
  command
  >
  >
  >
  >
  >
...

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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.

David Romano

5 Sep 5 Sep

10:32 a.m.

Thanks, Bruce and Doug; this raises other questions for me about mris_make_surfaces, but I'll ask those in a new thread.

Thanks again, David

On Wed, Sep 4, 2013 at 5:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

no, the smoothing is done irrespective of the intensity volume (in mris_smooth). The smoothness constraints in mris_make_surfaces are more sophisticated (they assume that the surfaces are well-fit by quadratic patches, not planes) and also move the surface to lie at large intensity gradients

On Wed, 4 Sep 2013, David Romano wrote:

Thanks, Doug; this helps me to formulate my second question better, which

...
is:

Assuming that no change in intensity is necessary, would the files

lh.white, lh.area, and lh.curv produced by the mri_make_surfaces command (in the -white subsection of the -autorecon2 section) be the same as the files produced by the command

mri_smooth lh.orig lh.white?

(Note that I dropped the flag -nw, so this will produce lh.area and lh.curv files.)

Thanks again, David

On Wed, Sep 4, 2013 at 4:10 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
  lh.orig.nofix is the original tesselation without anything done
  to it.
  To get to lh.white, the defects are automatically corrected to
  create
  lh.orig. lh.orig is then refined with smoothness and intensity
  constraints to produce lh.white
  doug


  On 09/04/2013 07:07 PM, David Romano wrote:
  > Hi everyone,
  >
  > I've been trying to go through the various steps described on
  the page:
  >
  > http://surfer.nmr.mgh.harvard.**edu/fswiki/ReconAllDevTable<http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable>
  >
  > and I'm trying to understand part of the -autorecon2 section,
  and in
  > particular,
  >
  > 1) how the lh.orig.nofix file that is produced by the end of
  the
  > -tessellate subsection is different from the the lh.white file
  that is
  > produced by the -white subsection, and
  >
  > 2) whether the area and curvature files produced by the
  command
  >
  >
  >
  >
  >
...
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

Douglas Greve

4 Sep 4 Sep

10:07 p.m.

No, that will just smooth the orig surface, it will not cause it to follow intensity gradients

On 9/4/13 7:56 PM, David Romano wrote:

...

Thanks, Doug; this helps me to formulate my second question better, which is:

Assuming that no change in intensity is necessary, would the files

lh.white, lh.area, and lh.curv produced by the mri_make_surfaces command (in the -white subsection of the -autorecon2 section) be the same as the files produced by the command

mri_smooth lh.orig lh.white?

(Note that I dropped the flag -nw, so this will produce lh.area and lh.curv files.)

Thanks again, David

On Wed, Sep 4, 2013 at 4:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

lh.orig.nofix is the original tesselation without anything done to it.
To get to lh.white, the defects are automatically corrected to create
lh.orig. lh.orig is then refined with smoothness and intensity
constraints to produce lh.white
doug

On 09/04/2013 07:07 PM, David Romano wrote:
> Hi everyone,
>
> I've been trying to go through the various steps described on
the page:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
>
> and I'm trying to understand part of the -autorecon2 section, and in
> particular,
>
> 1) how the lh.orig.nofix file that is produced by the end of the
> -tessellate subsection is different from the the lh.white file
that is
> produced by the -white subsection, and
>
> 2) whether the area and curvature files produced by the command
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto: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.

David Romano

7:12 p.m.

(Sorry -- inadvertently hit a key that triggered the "send" function. Here's the final version of the previous message:)

Hi everyone,

I've been trying to go through the various steps described on the page:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

and I'm trying to understand part of the -autorecon2 section, and in particular,

1) how the lh.orig.nofix file that is produced by the end of the -tessellate subsection is different from the the lh.white file that is produced by the -white subsection, and

2) how the area and curvature files produced by the command mris_smooth lh.orig.nofix lh.smoothwm.nofix would differ those produced by the -white subsection.

Thanks in advance for your help, David Romano

On Wed, Sep 4, 2013 at 4:07 PM, David Romano dromano@stanford.edu wrote:

...

Hi everyone,

I've been trying to go through the various steps described on the page:

http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

and I'm trying to understand part of the -autorecon2 section, and in particular,

how the lh.orig.nofix file that is produced by the end of the

-tessellate subsection is different from the the lh.white file that is produced by the -white subsection, and

whether the area and curvature files produced by the command

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Bruce Fischl
David Romano
Douglas Greve
Douglas N Greve