Hi Markus

I wouldn't use brainmask as it has been normalized too aggressivley. Maybe the nu.mgz. Look at the difference between values just outside of it and just inside of it

cheers Bruce

On Mon, 24 Mar 2014, Markus Gschwind wrote:

Dear Bruce, Thanks for the rapid answer!

Do you mean that I take the voxel values of brainmask.mgz at the place where the ?h.white surface passes, right?

I thought that the ?l.white surface marks the limit between GM and WM as a result of a binary decision.  I would be interested in the local certainty of this decision. I thought this is represented by the slope between the values around 70 and those

...

100.

Thanks again,  Markus

2014-03-24 19:26 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Markus

  I would think that looking at the gray/white contrast across the
  ?h.white surface would be more informative

  cheers
  Bruce
  On Mon, 24 Mar 2014, Markus Gschwind wrote:

        Dear all,
        I would like to capture regions where the gray
        matter/ white matter junction is blurred in order to
        detect possible focal
        cortical dysplasias.

        As I understood the WM/GM segmentation is done by
        the script mri_segment.

        Would it be possible detect those regions where the
        gradient between GM and WM regions is low? 

        I imagined that running mri_segment several times,
        with each time a different lower GM threshold and
        higher WM threshold, and
        then calculating the diference between the results,
        might give such information.

        I am very much interested in what you think about
        this approach and how to do it practically.

        For info here are the optional flags of mri_segment:

        -slope <s>

        set the curvature slope (both n and p)

        -pslope <p>

        set the curvature pslope (default=1.0)

        -nslope <n>

        set the curvature nslope (default=1.0)

        -debug_voxel <x y z>

        set voxel for debugging

        -auto

        automatically detect class statistics (default)

        -noauto

        don't automatically detect class statistics

        -log

        log to ./segment.dat

        -keep

        keep wm edits. maintains all values of 0 and 255

        -ghi, -gray_hi <h>

        set the gray matter high limit (default=100.000)

        -wlo, -wm_low <l>

        set the white matter low limit (default=90.000)

        -whi, -wm_hi <h>

        set the white matter high limit (default=125.000)

        -nseg <n>

        thicken the n largest thin strands (default=20)

        -thicken

        toggle thickening step (default=ON)

        -fillbg

        toggle filling of the basal ganglia (default=OFF)

        -fillv

        toggle filling of the ventricles (default=OFF)

        -b <s>

        set blur sigma (default=0.25)

        -n <i>

        set # iterations of border classification
        (default=1)

        -t <t>

        set limit to thin strands in mm (default=4)

        -v

        verbose

        -p <p>

        set % threshold (default=0.80)

        -x <filename>

        extract options from filename

        -w <w>

        set wsize (default=11)

        -u

        usage

         

        Thank you very much for all comments!

        Markus

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it really depends on the size of the abnormality. I would guess 2 is too big, and you want something more like 1, and sampling not averaging On Mon, 24 Mar 2014, Markus Gschwind wrote:

Hi Bruce! Ok I see, great! Tank you!

So to double check, this will be something like :

mri_vol2surf \

--mov /mri/nu.mgz \ --ref /mri/nu.mgz \

--surf /surf/lh.white --projdist mmdist -2 \ # for inside white

# --projdist mmdist 2 \ # for outside white --interp trilinear \ --hemi lh \ --out lh.nu_inside_white.mgh

I am not sure which one to use from those, as I want to compare stable values but distant from white.

--projfrac-avg min max del : average along normal --projdist mmdist : distance projection along normal --projdist-avg min max del : average along normal

What would you recommend? Thank you again! Markus

2014-03-24 21:29 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Markus

  I wouldn't use brainmask as it has been normalized too
  aggressivley. Maybe the nu.mgz. Look at the difference between
  values just outside of it and just inside of it

  cheers
  Bruce


  On Mon, 24 Mar 2014, Markus Gschwind wrote:

        Dear Bruce,
        Thanks for the rapid answer!

        Do you mean that I take the voxel values of
        brainmask.mgz at the place where
        the ?h.white surface passes, right?

        I thought that the ?l.white surface marks the limit
        between GM and WM as a
        result of a binary decision. 
        I would be interested in the local certainty of this
        decision. I thought
        this is represented by the slope between the values
        around 70 and those
        >100. 

        Thanks again, 
        Markus






        2014-03-24 19:26 GMT+01:00 Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>:
              Hi Markus

              I would think that looking at the gray/white
        contrast across the
              ?h.white surface would be more informative

              cheers
              Bruce
              On Mon, 24 Mar 2014, Markus Gschwind wrote:

                    Dear all,
                    I would like to capture regions where
        the gray
                    matter/ white matter junction is blurred
        in order to
                    detect possible focal
                    cortical dysplasias.

                    As I understood the WM/GM segmentation
        is done by
                    the script mri_segment.

                    Would it be possible detect those
        regions where the
                    gradient between GM and WM regions is
        low? 

                    I imagined that running mri_segment
        several times,
                    with each time a different lower GM
        threshold and
                    higher WM threshold, and
                    then calculating the diference between
        the results,
                    might give such information.

                    I am very much interested in what you
        think about
                    this approach and how to do it
        practically.

                    For info here are the optional flags of
        mri_segment:

                    -slope <s>

                    set the curvature slope (both n and p)

                    -pslope <p>

                    set the curvature pslope (default=1.0)

                    -nslope <n>

                    set the curvature nslope (default=1.0)

                    -debug_voxel <x y z>

                    set voxel for debugging

                    -auto

                    automatically detect class statistics
        (default)

                    -noauto

                    don't automatically detect class
        statistics

                    -log

                    log to ./segment.dat

                    -keep

                    keep wm edits. maintains all values of 0
        and 255

                    -ghi, -gray_hi <h>

                    set the gray matter high limit
        (default=100.000)

                    -wlo, -wm_low <l>

                    set the white matter low limit
        (default=90.000)

                    -whi, -wm_hi <h>

                    set the white matter high limit
        (default=125.000)

                    -nseg <n>

                    thicken the n largest thin strands
        (default=20)

                    -thicken

                    toggle thickening step (default=ON)

                    -fillbg

                    toggle filling of the basal ganglia
        (default=OFF)

                    -fillv

                    toggle filling of the ventricles
        (default=OFF)

                    -b <s>

                    set blur sigma (default=0.25)

                    -n <i>

                    set # iterations of border
        classification
                    (default=1)

                    -t <t>

                    set limit to thin strands in mm
        (default=4)

                    -v

                    verbose

                    -p <p>

                    set % threshold (default=0.80)

                    -x <filename>

                    extract options from filename

                    -w <w>

                    set wsize (default=11)

                    -u

                    usage

                     

                    Thank you very much for all comments!

                    Markus


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        it is
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        e-mail
        contains patient information, please contact the
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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.

Whow that is great!! Thank you so much Doug, I was not aware of this! That's what I needed it seems. Thanks Bruce and Doug! Markus

2014-03-24 23:21 GMT+01:00 Douglas N Greve greve@nmr.mgh.harvard.edu:

you might want to look at the pctsurfcon script to see if that gets you where you want to be

On 03/24/2014 06:18 PM, Bruce Fischl wrote:

...

it really depends on the size of the abnormality. I would guess 2 is too big, and you want something more like 1, and sampling not averaging On Mon, 24 Mar 2014, Markus Gschwind wrote:

...

Hi Bruce! Ok I see, great! Tank you!

So to double check, this will be something like :

mri_vol2surf \

--mov /mri/nu.mgz \ --ref /mri/nu.mgz \

--surf /surf/lh.white --projdist mmdist -2 \ # for inside white

# --projdist mmdist 2 \ # for outside white --interp trilinear \ --hemi lh \ --out lh.nu_inside_white.mgh

I am not sure which one to use from those, as I want to compare stable values but distant from white.

--projfrac-avg min max del : average along normal --projdist mmdist : distance projection along normal --projdist-avg min max del : average along normal

What would you recommend? Thank you again! Markus

2014-03-24 21:29 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Markus

  I wouldn't use brainmask as it has been normalized too
  aggressivley. Maybe the nu.mgz. Look at the difference between
  values just outside of it and just inside of it

  cheers
  Bruce


  On Mon, 24 Mar 2014, Markus Gschwind wrote:

        Dear Bruce,
        Thanks for the rapid answer!

        Do you mean that I take the voxel values of
        brainmask.mgz at the place where
        the ?h.white surface passes, right?

        I thought that the ?l.white surface marks the limit
        between GM and WM as a
        result of a binary decision.
        I would be interested in the local certainty of this
        decision. I thought
        this is represented by the slope between the values
        around 70 and those
        >100.

        Thanks again,
        Markus






        2014-03-24 19:26 GMT+01:00 Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>:
              Hi Markus

              I would think that looking at the gray/white
        contrast across the
              ?h.white surface would be more informative

              cheers
              Bruce
              On Mon, 24 Mar 2014, Markus Gschwind wrote:

                    Dear all,
                    I would like to capture regions where
        the gray
                    matter/ white matter junction is blurred
        in order to
                    detect possible focal
                    cortical dysplasias.

                    As I understood the WM/GM segmentation
        is done by
                    the script mri_segment.

                    Would it be possible detect those
        regions where the
                    gradient between GM and WM regions is
        low?

                    I imagined that running mri_segment
        several times,
                    with each time a different lower GM
        threshold and
                    higher WM threshold, and
                    then calculating the diference between
        the results,
                    might give such information.

                    I am very much interested in what you
        think about
                    this approach and how to do it
        practically.

                    For info here are the optional flags of
        mri_segment:

                    -slope <s>

                    set the curvature slope (both n and p)

                    -pslope <p>

                    set the curvature pslope (default=1.0)

                    -nslope <n>

                    set the curvature nslope (default=1.0)

                    -debug_voxel <x y z>

                    set voxel for debugging

                    -auto

                    automatically detect class statistics
        (default)

                    -noauto

                    don't automatically detect class
        statistics

                    -log

                    log to ./segment.dat

                    -keep

                    keep wm edits. maintains all values of 0
        and 255

                    -ghi, -gray_hi <h>

                    set the gray matter high limit
        (default=100.000)

                    -wlo, -wm_low <l>

                    set the white matter low limit
        (default=90.000)

                    -whi, -wm_hi <h>

                    set the white matter high limit
        (default=125.000)

                    -nseg <n>

                    thicken the n largest thin strands
        (default=20)

                    -thicken

                    toggle thickening step (default=ON)

                    -fillbg

                    toggle filling of the basal ganglia
        (default=OFF)

                    -fillv

                    toggle filling of the ventricles
        (default=OFF)

                    -b <s>

                    set blur sigma (default=0.25)

                    -n <i>

                    set # iterations of border
        classification
                    (default=1)

                    -t <t>

                    set limit to thin strands in mm
        (default=4)

                    -v

                    verbose

                    -p <p>

                    set % threshold (default=0.80)

                    -x <filename>

                    extract options from filename

                    -w <w>

                    set wsize (default=11)

                    -u

                    usage



                    Thank you very much for all comments!

                    Markus


        _______________________________________________
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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.

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On 3/26/14 8:24 AM, Markus Gschwind wrote:

Dear Doug and Bruce,

I have three more questions concerning 'pctsurfcon'.

1. The inner sampling distance is set to 1mm by default, but the outer

sampling is done at a 30% of the cortical thickness. I saw that I could easily change the parameters or modify the script, but I wonder why this has been chosen like this. What was the rationale?

A fixed distance of 1mm was used to help prevent the WM sample from projecting so far back that it samples GM "behind" it. I can't remember how I choose 30% (instead of 50%). I think David Salat used slightly different parameters in his paper.

2. I think it is possible to run glmfit on the ?h.w-g.pct.mgh file in

order to get some group stats, right?

Yes

3. Is it also possibe to run the xhemi on the w-g.pct.mgh file?

Yes doug

Thank you so much! Markus

2014-03-24 23:51 GMT+01:00 Markus Gschwind <markus.gschwind@gmail.com mailto:markus.gschwind@gmail.com>:

Whow that is great!! Thank you so much Doug, I was not aware of
this! That's what I needed it seems.
Thanks Bruce and Doug!
Markus


2014-03-24 23:21 GMT+01:00 Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>:


    you might want to look at the pctsurfcon script to see if that
    gets you
    where you want to be

    On 03/24/2014 06:18 PM, Bruce Fischl wrote:
    > it really depends on the size of the abnormality. I would
    guess 2 is
    > too big, and you want something more like 1, and sampling
    not averaging
    > On Mon, 24 Mar 2014, Markus Gschwind wrote:
    >
    >> Hi Bruce!
    >> Ok I see, great! Tank you!
    >>
    >> So to double check, this will be something like :
    >>
    >> mri_vol2surf \
    >>
    >>
    >>   --mov /mri/nu.mgz \
    >>   --ref /mri/nu.mgz \
    >>
    >>   --surf /surf/lh.white
    >>   --projdist mmdist -2 \ # for inside white
    >>
    >>
    >>   # --projdist mmdist 2 \ # for outside white
    >>   --interp trilinear \
    >>   --hemi lh \
    >>   --out lh.nu_inside_white.mgh
    >>
    >>
    >> I am not sure which one to use from those, as I want to
    compare stable
    >> values but distant from white.
    >>
    >>
    >>    --projfrac-avg min max del : average along normal
    >>    --projdist mmdist : distance projection along normal
    >>    --projdist-avg min max del : average along normal
    >>
    >> What would you recommend?
    >> Thank you again!
    >> Markus
    >>
    >>
    >>
    >>
    >>
    >>
    >>
    >> 2014-03-24 21:29 GMT+01:00 Bruce Fischl
    <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>:
    >>       Hi Markus
    >>
    >>       I wouldn't use brainmask as it has been normalized too
    >>       aggressivley. Maybe the nu.mgz. Look at the
    difference between
    >>       values just outside of it and just inside of it
    >>
    >>       cheers
    >>       Bruce
    >>
    >>
    >>       On Mon, 24 Mar 2014, Markus Gschwind wrote:
    >>
    >>             Dear Bruce,
    >>             Thanks for the rapid answer!
    >>
    >>             Do you mean that I take the voxel values of
    >>             brainmask.mgz at the place where
    >>             the ?h.white surface passes, right?
    >>
    >>             I thought that the ?l.white surface marks the limit
    >>             between GM and WM as a
    >>             result of a binary decision.
    >>             I would be interested in the local certainty of
    this
    >>             decision. I thought
    >>             this is represented by the slope between the values
    >>             around 70 and those
    >>             >100.
    >>
    >>             Thanks again,
    >>             Markus
    >>
    >>
    >>
    >>
    >>
    >>
    >>             2014-03-24 19:26 GMT+01:00 Bruce Fischl
    >>             <fischl@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>>:
    >>                   Hi Markus
    >>
    >>                   I would think that looking at the gray/white
    >>             contrast across the
    >>                   ?h.white surface would be more informative
    >>
    >>                   cheers
    >>                   Bruce
    >>                   On Mon, 24 Mar 2014, Markus Gschwind wrote:
    >>
    >>                         Dear all,
    >>                         I would like to capture regions where
    >>             the gray
    >>                         matter/ white matter junction is
    blurred
    >>             in order to
    >>                         detect possible focal
    >>                         cortical dysplasias.
    >>
    >>                         As I understood the WM/GM segmentation
    >>             is done by
    >>                         the script mri_segment.
    >>
    >>                         Would it be possible detect those
    >>             regions where the
    >>                         gradient between GM and WM regions is
    >>             low?
    >>
    >>                         I imagined that running mri_segment
    >>             several times,
    >>                         with each time a different lower GM
    >>             threshold and
    >>                         higher WM threshold, and
    >>                         then calculating the diference between
    >>             the results,
    >>                         might give such information.
    >>
    >>                         I am very much interested in what you
    >>             think about
    >>                         this approach and how to do it
    >>             practically.
    >>
    >>                         For info here are the optional flags of
    >>             mri_segment:
    >>
    >>                         -slope <s>
    >>
    >>                         set the curvature slope (both n and p)
    >>
    >>                         -pslope <p>
    >>
    >>                         set the curvature pslope (default=1.0)
    >>
    >>                         -nslope <n>
    >>
    >>                         set the curvature nslope (default=1.0)
    >>
    >>                         -debug_voxel <x y z>
    >>
    >>                         set voxel for debugging
    >>
    >>                         -auto
    >>
    >>                         automatically detect class statistics
    >>             (default)
    >>
    >>                         -noauto
    >>
    >>                         don't automatically detect class
    >>             statistics
    >>
    >>                         -log
    >>
    >>                         log to ./segment.dat
    >>
    >>                         -keep
    >>
    >>                         keep wm edits. maintains all values
    of 0
    >>             and 255
    >>
    >>                         -ghi, -gray_hi <h>
    >>
    >>                         set the gray matter high limit
    >>             (default=100.000)
    >>
    >>                         -wlo, -wm_low <l>
    >>
    >>                         set the white matter low limit
    >>             (default=90.000)
    >>
    >>                         -whi, -wm_hi <h>
    >>
    >>                         set the white matter high limit
    >>             (default=125.000)
    >>
    >>                         -nseg <n>
    >>
    >>                         thicken the n largest thin strands
    >>             (default=20)
    >>
    >>                         -thicken
    >>
    >>                         toggle thickening step (default=ON)
    >>
    >>                         -fillbg
    >>
    >>                         toggle filling of the basal ganglia
    >>             (default=OFF)
    >>
    >>                         -fillv
    >>
    >>                         toggle filling of the ventricles
    >>             (default=OFF)
    >>
    >>                         -b <s>
    >>
    >>                         set blur sigma (default=0.25)
    >>
    >>                         -n <i>
    >>
    >>                         set # iterations of border
    >>             classification
    >>                         (default=1)
    >>
    >>                         -t <t>
    >>
    >>                         set limit to thin strands in mm
    >>             (default=4)
    >>
    >>                         -v
    >>
    >>                         verbose
    >>
    >>                         -p <p>
    >>
    >>                         set % threshold (default=0.80)
    >>
    >>                         -x <filename>
    >>
    >>                         extract options from filename
    >>
    >>                         -w <w>
    >>
    >>                         set wsize (default=11)
    >>
    >>                         -u
    >>
    >>                         usage
    >>
    >>
    >>
    >>                         Thank you very much for all comments!
    >>
    >>                         Markus
    >>
    >>
    >> _______________________________________________
    >>             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.
    >>
    >>
    >>
    >>
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Hi Markus

use mris_expand.

cheers Bruce On Thu, 27 Mar 2014, Markus Gschwind wrote:

Thank you, Doug! One last question:

• Using which command would one construct the "?h.white -1mm surface" and

the "?h.white+30%GM surface" for visualisation purposes as in Salat  Figure 1(http://www.sciencedirect.com/science/article/pii/S1053811910013261?via=ihu b)?

Thank you! Markus

2014-03-26 15:36 GMT+01:00 Douglas Greve greve@nmr.mgh.harvard.edu:

  On 3/26/14 8:24 AM, Markus Gschwind wrote:
  Dear Doug and Bruce,

I have three more questions concerning 'pctsurfcon'.

1. The inner sampling distance is set to 1mm by default, but the

outer sampling is done at a 30% of the cortical thickness. I saw that I could easily change the parameters or modify the script, but I wonder why this has been chosen like this. What was the rationale?

A fixed distance of 1mm was used to help prevent the WM sample from projecting so far back that it samples GM "behind" it. I can't remember how I choose 30% (instead of 50%). I think David Salat used slightly different parameters in his paper.

2. I think it is possible to run glmfit on the ?h.w-g.pct.mgh

file in order to get some group stats, right?

Yes

3. Is it also possibe to run the xhemi on the w-g.pct.mgh file?

Yes doug

Thank you so much! Markus

2014-03-24 23:51 GMT+01:00 Markus Gschwind markus.gschwind@gmail.com: Whow that is great!! Thank you so much Doug, I was not aware of this! That's what I needed it seems.  Thanks Bruce and Doug! Markus

2014-03-24 23:21 GMT+01:00 Douglas N Greve greve@nmr.mgh.harvard.edu:

  you might want to look at the pctsurfcon
  script to see if that gets you
  where you want to be

  On 03/24/2014 06:18 PM, Bruce Fischl wrote:
  > it really depends on the size of the
  abnormality. I would guess 2 is
  > too big, and you want something more like 1,
  and sampling not averaging
  > On Mon, 24 Mar 2014, Markus Gschwind wrote:
  >
  >> Hi Bruce!
  >> Ok I see, great! Tank you!
  >>
  >> So to double check, this will be something
  like :
  >>
  >> mri_vol2surf \
  >>
  >>
  >>   --mov /mri/nu.mgz \
  >>   --ref /mri/nu.mgz \
  >>
  >>   --surf /surf/lh.white
  >>   --projdist mmdist -2 \ # for inside white
  >>
  >>
  >>   # --projdist mmdist 2 \ # for outside
  white
  >>   --interp trilinear \
  >>   --hemi lh \
  >>   --out lh.nu_inside_white.mgh
  >>
  >>
  >> I am not sure which one to use from those,
  as I want to compare stable
  >> values but distant from white.
  >>
  >>
  >>    --projfrac-avg min max del : average
  along normal
  >>    --projdist mmdist : distance projection
  along normal
  >>    --projdist-avg min max del : average
  along normal
  >>
  >> What would you recommend?
  >> Thank you again!
  >> Markus
  >>
  >>
  >>
  >>
  >>
  >>
  >>
  >> 2014-03-24 21:29 GMT+01:00 Bruce Fischl
  <fischl@nmr.mgh.harvard.edu>:
  >>       Hi Markus
  >>
  >>       I wouldn't use brainmask as it has
  been normalized too
  >>       aggressivley. Maybe the nu.mgz. Look
  at the difference between
  >>       values just outside of it and just
  inside of it
  >>
  >>       cheers
  >>       Bruce
  >>
  >>
  >>       On Mon, 24 Mar 2014, Markus Gschwind
  wrote:
  >>
  >>             Dear Bruce,
  >>             Thanks for the rapid answer!
  >>
  >>             Do you mean that I take the
  voxel values of
  >>             brainmask.mgz at the place
  where
  >>             the ?h.white surface passes,
  right?
  >>
  >>             I thought that the ?l.white
  surface marks the limit
  >>             between GM and WM as a
  >>             result of a binary decision.
  >>             I would be interested in the
  local certainty of this
  >>             decision. I thought
  >>             this is represented by the
  slope between the values
  >>             around 70 and those
  >>             >100.
  >>
  >>             Thanks again,
  >>             Markus
  >>
  >>
  >>
  >>
  >>
  >>
  >>             2014-03-24 19:26 GMT+01:00
  Bruce Fischl
  >>             <fischl@nmr.mgh.harvard.edu>:
  >>                   Hi Markus
  >>
  >>                   I would think that
  looking at the gray/white
  >>             contrast across the
  >>                   ?h.white surface would be
  more informative
  >>
  >>                   cheers
  >>                   Bruce
  >>                   On Mon, 24 Mar 2014,
  Markus Gschwind wrote:
  >>
  >>                         Dear all,
  >>                         I would like to
  capture regions where
  >>             the gray
  >>                         matter/ white
  matter junction is blurred
  >>             in order to
  >>                         detect possible
  focal
  >>                         cortical
  dysplasias.
  >>
  >>                         As I understood the
  WM/GM segmentation
  >>             is done by
  >>                         the script
  mri_segment.
  >>
  >>                         Would it be
  possible detect those
  >>             regions where the
  >>                         gradient between GM
  and WM regions is
  >>             low?
  >>
  >>                         I imagined that
  running mri_segment
  >>             several times,
  >>                         with each time a
  different lower GM
  >>             threshold and
  >>                         higher WM
  threshold, and
  >>                         then calculating
  the diference between
  >>             the results,
  >>                         might give such
  information.
  >>
  >>                         I am very much
  interested in what you
  >>             think about
  >>                         this approach and
  how to do it
  >>             practically.
  >>
  >>                         For info here are
  the optional flags of
  >>             mri_segment:
  >>
  >>                         -slope <s>
  >>
  >>                         set the curvature
  slope (both n and p)
  >>
  >>                         -pslope <p>
  >>
  >>                         set the curvature
  pslope (default=1.0)
  >>
  >>                         -nslope <n>
  >>
  >>                         set the curvature
  nslope (default=1.0)
  >>
  >>                         -debug_voxel <x y
  z>
  >>
  >>                         set voxel for
  debugging
  >>
  >>                         -auto
  >>
  >>                         automatically
  detect class statistics
  >>             (default)
  >>
  >>                         -noauto
  >>
  >>                         don't automatically
  detect class
  >>             statistics
  >>
  >>                         -log
  >>
  >>                         log to
  ./segment.dat
  >>
  >>                         -keep
  >>
  >>                         keep wm edits.
  maintains all values of 0
  >>             and 255
  >>
  >>                         -ghi, -gray_hi <h>
  >>
  >>                         set the gray matter
  high limit
  >>             (default=100.000)
  >>
  >>                         -wlo, -wm_low <l>
  >>
  >>                         set the white
  matter low limit
  >>             (default=90.000)
  >>
  >>                         -whi, -wm_hi <h>
  >>
  >>                         set the white
  matter high limit
  >>             (default=125.000)
  >>
  >>                         -nseg <n>
  >>
  >>                         thicken the n
  largest thin strands
  >>             (default=20)
  >>
  >>                         -thicken
  >>
  >>                         toggle thickening
  step (default=ON)
  >>
  >>                         -fillbg
  >>
  >>                         toggle filling of
  the basal ganglia
  >>             (default=OFF)
  >>
  >>                         -fillv
  >>
  >>                         toggle filling of
  the ventricles
  >>             (default=OFF)
  >>
  >>                         -b <s>
  >>
  >>                         set blur sigma
  (default=0.25)
  >>
  >>                         -n <i>
  >>
  >>                         set # iterations of
  border
  >>             classification
  >>                         (default=1)
  >>
  >>                         -t <t>
  >>
  >>                         set limit to thin
  strands in mm
  >>             (default=4)
  >>
  >>                         -v
  >>
  >>                         verbose
  >>
  >>                         -p <p>
  >>
  >>                         set % threshold
  (default=0.80)
  >>
  >>                         -x <filename>
  >>
  >>                         extract options
  from filename
  >>
  >>                         -w <w>
  >>
  >>                         set wsize
  (default=11)
  >>
  >>                         -u
  >>
  >>                         usage
  >>
  >>
  >>
  >>                         Thank you very much
  for all comments!
  >>
  >>                         Markus
  >>
  >>
  >>            
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glad it worked out Bruce On Fri, 28 Mar 2014, Markus Gschwind wrote:

Thank you Bruce, this works great. This is just for the records:

  $ mris_expand -thickness surf/lh.white 0.35
  surf/lh.white_outer0.35GM
  using distance as a % of thickness
  expanding surface surf/lh.white by 35.0% of thickness and
  writing it to surf/lh.white_outer0.35GM

$ mris_expand surf/lh.white -1 surf/lh.white_inner1mmWM expanding surface surf/lh.white by -1.0 mm and writing it to surf/lh.white_inner1mmWM

Thanks again!

2014-03-27 13:29 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Markus

  use mris_expand.

  cheers
  Bruce
  On Thu, 27 Mar 2014, Markus Gschwind wrote:

        Thank you, Doug!
        One last question: 
        - Using which command would one construct the
        "?h.white -1mm surface" and
        the "?h.white+30%GM surface" for visualisation
        purposes as in Salat  Figure

1(http://www.sciencedirect.com/science/article/pii/S1053811910013261?via=ih u b)?

        Thank you!
        Markus



        2014-03-26 15:36 GMT+01:00 Douglas Greve
        <greve@nmr.mgh.harvard.edu>:

              On 3/26/14 8:24 AM, Markus Gschwind wrote:
              Dear Doug and Bruce,
        I have three more questions concerning 'pctsurfcon'.

        1) The inner sampling distance is set to 1mm by
        default, but the
        outer sampling is done at a 30% of the cortical
        thickness. I saw
        that I could easily change the parameters or modify
        the script,
        but I wonder why this has been chosen like this.
        What was the
        rationale?

        A fixed distance of 1mm was used to help prevent the
        WM sample from
        projecting so far back that it samples GM "behind"
        it. I can't
        remember how I choose 30% (instead of 50%). I think
        David Salat used
        slightly different parameters in his paper. 



        2) I think it is possible to run glmfit on the
        ?h.w-g.pct.mgh
        file in order to get some group stats, right?

        Yes

        3) Is it also possibe to run the xhemi on the
        w-g.pct.mgh file?

        Yes
        doug


        Thank you so much!
        Markus


        2014-03-24 23:51 GMT+01:00 Markus Gschwind
        <markus.gschwind@gmail.com>:
              Whow that is great!! Thank you so much Doug, I
        was
              not aware of this! That's what I needed it
        seems. 
              Thanks Bruce and Doug!
        Markus


        2014-03-24 23:21 GMT+01:00 Douglas N Greve
        <greve@nmr.mgh.harvard.edu>:

              you might want to look at the pctsurfcon
              script to see if that gets you
              where you want to be

              On 03/24/2014 06:18 PM, Bruce Fischl wrote:
              > it really depends on the size of the
              abnormality. I would guess 2 is
              > too big, and you want something more like 1,
              and sampling not averaging
              > On Mon, 24 Mar 2014, Markus Gschwind wrote:
              >
              >> Hi Bruce!
              >> Ok I see, great! Tank you!
              >>
              >> So to double check, this will be something
              like :
              >>
              >> mri_vol2surf \
              >>
              >>
              >>   --mov /mri/nu.mgz \
              >>   --ref /mri/nu.mgz \
              >>
              >>   --surf /surf/lh.white
              >>   --projdist mmdist -2 \ # for inside white
              >>
              >>
              >>   # --projdist mmdist 2 \ # for outside
              white
              >>   --interp trilinear \
              >>   --hemi lh \
              >>   --out lh.nu_inside_white.mgh
              >>
              >>
              >> I am not sure which one to use from those,
              as I want to compare stable
              >> values but distant from white.
              >>
              >>
              >>    --projfrac-avg min max del : average
              along normal
              >>    --projdist mmdist : distance projection
              along normal
              >>    --projdist-avg min max del : average
              along normal
              >>
              >> What would you recommend?
              >> Thank you again!
              >> Markus
              >>
              >>
              >>
              >>
              >>
              >>
              >>
              >> 2014-03-24 21:29 GMT+01:00 Bruce Fischl
              <fischl@nmr.mgh.harvard.edu>:
              >>       Hi Markus
              >>
              >>       I wouldn't use brainmask as it has
              been normalized too
              >>       aggressivley. Maybe the nu.mgz. Look
              at the difference between
              >>       values just outside of it and just
              inside of it
              >>
              >>       cheers
              >>       Bruce
              >>
              >>
              >>       On Mon, 24 Mar 2014, Markus Gschwind
              wrote:
              >>
              >>             Dear Bruce,
              >>             Thanks for the rapid answer!
              >>
              >>             Do you mean that I take the
              voxel values of
              >>             brainmask.mgz at the place
              where
              >>             the ?h.white surface passes,
              right?
              >>
              >>             I thought that the ?l.white
              surface marks the limit
              >>             between GM and WM as a
              >>             result of a binary decision.
              >>             I would be interested in the
              local certainty of this
              >>             decision. I thought
              >>             this is represented by the
              slope between the values
              >>             around 70 and those
              >>             >100.
              >>
              >>             Thanks again,
              >>             Markus
              >>
              >>
              >>
              >>
              >>
              >>
              >>             2014-03-24 19:26 GMT+01:00
              Bruce Fischl
              >>             <fischl@nmr.mgh.harvard.edu>:
              >>                   Hi Markus
              >>
              >>                   I would think that
              looking at the gray/white
              >>             contrast across the
              >>                   ?h.white surface would be
              more informative
              >>
              >>                   cheers
              >>                   Bruce
              >>                   On Mon, 24 Mar 2014,
              Markus Gschwind wrote:
              >>
              >>                         Dear all,
              >>                         I would like to
              capture regions where
              >>             the gray
              >>                         matter/ white
              matter junction is blurred
              >>             in order to
              >>                         detect possible
              focal
              >>                         cortical
              dysplasias.
              >>
              >>                         As I understood the
              WM/GM segmentation
              >>             is done by
              >>                         the script
              mri_segment.
              >>
              >>                         Would it be
              possible detect those
              >>             regions where the
              >>                         gradient between GM
              and WM regions is
              >>             low?
              >>
              >>                         I imagined that
              running mri_segment
              >>             several times,
              >>                         with each time a
              different lower GM
              >>             threshold and
              >>                         higher WM
              threshold, and
              >>                         then calculating
              the diference between
              >>             the results,
              >>                         might give such
              information.
              >>
              >>                         I am very much
              interested in what you
              >>             think about
              >>                         this approach and
              how to do it
              >>             practically.
              >>
              >>                         For info here are
              the optional flags of
              >>             mri_segment:
              >>
              >>                         -slope <s>
              >>
              >>                         set the curvature
              slope (both n and p)
              >>
              >>                         -pslope <p>
              >>
              >>                         set the curvature
              pslope (default=1.0)
              >>
              >>                         -nslope <n>
              >>
              >>                         set the curvature
              nslope (default=1.0)
              >>
              >>                         -debug_voxel <x y
              z>
              >>
              >>                         set voxel for
              debugging
              >>
              >>                         -auto
              >>
              >>                         automatically
              detect class statistics
              >>             (default)
              >>
              >>                         -noauto
              >>
              >>                         don't automatically
              detect class
              >>             statistics
              >>
              >>                         -log
              >>
              >>                         log to
              ./segment.dat
              >>
              >>                         -keep
              >>
              >>                         keep wm edits.
              maintains all values of 0
              >>             and 255
              >>
              >>                         -ghi, -gray_hi <h>
              >>
              >>                         set the gray matter
              high limit
              >>             (default=100.000)
              >>
              >>                         -wlo, -wm_low <l>
              >>
              >>                         set the white
              matter low limit
              >>             (default=90.000)
              >>
              >>                         -whi, -wm_hi <h>
              >>
              >>                         set the white
              matter high limit
              >>             (default=125.000)
              >>
              >>                         -nseg <n>
              >>
              >>                         thicken the n
              largest thin strands
              >>             (default=20)
              >>
              >>                         -thicken
              >>
              >>                         toggle thickening
              step (default=ON)
              >>
              >>                         -fillbg
              >>
              >>                         toggle filling of
              the basal ganglia
              >>             (default=OFF)
              >>
              >>                         -fillv
              >>
              >>                         toggle filling of
              the ventricles
              >>             (default=OFF)
              >>
              >>                         -b <s>
              >>
              >>                         set blur sigma
              (default=0.25)
              >>
              >>                         -n <i>
              >>
              >>                         set # iterations of
              border
              >>             classification
              >>                         (default=1)
              >>
              >>                         -t <t>
              >>
              >>                         set limit to thin
              strands in mm
              >>             (default=4)
              >>
              >>                         -v
              >>
              >>                         verbose
              >>
              >>                         -p <p>
              >>
              >>                         set % threshold
              (default=0.80)
              >>
              >>                         -x <filename>
              >>
              >>                         extract options
              from filename
              >>
              >>                         -w <w>
              >>
              >>                         set wsize
              (default=11)
              >>
              >>                         -u
              >>
              >>                         usage
              >>
              >>
              >>
              >>                         Thank you very much
              for all comments!
              >>
              >>                         Markus
              >>
              >>
              >>            
             
        _______________________________________________
              >>             Freesurfer mailing list
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              >>
             
        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.
              >>
              >>
              >>
              >>
              >>
             
        _______________________________________________
              >> 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.
              >>
              >>
              >>
              >>
              >
              >
              >
             
        _______________________________________________
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              >
             
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        --
        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
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        it is
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        e-mail
        contains patient information, please contact the
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