overlay mni152 activation -- difference between tksurfer and freeview

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Re: [Freesurfer] overlay mni152...

DODS slope information

Yang, Daniel

25 Sep 2013 25 Sep '13

8:31 a.m.

Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold...

Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Douglas N Greve

26 Sep 26 Sep

12:26 p.m.

They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote:

...

Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold...

Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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/

Yang, Daniel

27 Sep 27 Sep

6:44 a.m.

Thanks Doug!

Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use?

Is it some sort of inverse mni152.register.dat?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/26/13 12:26 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote: Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold...

Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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/

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.

Yang, Daniel

1 Oct 1 Oct

5:49 p.m.

Hi Doug,

Just checking again, because I haven't heard from you. So the purpose is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure about the correct register.dat to use. The mni152.register.dat is for MNI305 -> MNI152 though.

I'm assuming that there exists some sort of inverse mni152.register.dat somewhere?

Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/27/13 6:44 AM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:

Thanks Doug!

Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use?

Is it some sort of inverse mni152.register.dat?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/26/13 12:26 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold...

Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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

Douglas N Greve

6 p.m.

The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces

doug

On 10/01/2013 05:49 PM, Yang, Daniel wrote:

...

Hi Doug,

I'm assuming that there exists some sort of inverse mni152.register.dat somewhere?

Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/27/13 6:44 AM, "Yang, Daniel" <yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu> wrote:

Thanks Doug!

Because it maps from a MNI152 space to the FreeSurfer average
space, do you know what register.dat I can use?

Is it some sort of inverse mni152.register.dat?
Thanks!
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/26/13 12:26 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>> wrote:

    They might be sampling to different surfaces. To make sure
    they show the
    same exact thing, try mapping the data to the surface with
    mri_vol2surf
    doug
    On 09/25/2013 08:31 AM, Yang, Daniel wrote:

        Dear FreeSurfer Experts,

        I am trying to visualize fMRI activation (generated from
        fsl) on the
        fsaverage inflated surface, using mni152.register.dat.

        It's odd that I find the results to be slightly different
        between
        tksurfer and freeview. However, I made sure that I am
        using the same
        threshold...

        Judging from fslview, I think the result with freeview is
        more
        accurate -- is it due to tksurfer loading orig.mgz by
        default, and
        free view loading something else?

        Thanks!
        Daniel

        -- 
        Yung-Jui "Daniel" Yang, PhD
        Postdoctoral Researcher
        Yale Child Study Center
        New Haven, CT
        (203) 737-5454


        _______________________________________________
        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
    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
    <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
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Yang, Daniel

6:10 p.m.

Hi Doug,

I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 10/1/13 6:00 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces

doug

On 10/01/2013 05:49 PM, Yang, Daniel wrote: Hi Doug,

I'm assuming that there exists some sort of inverse mni152.register.dat somewhere?

Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/27/13 6:44 AM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu> wrote:

Thanks Doug!

Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use?

Is it some sort of inverse mni152.register.dat? Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/26/13 12:26 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold...

Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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

Douglas N Greve

6:11 p.m.

I don't understand what you mean by a "much smaller brain". Can you elaborate? On 10/01/2013 06:10 PM, Yang, Daniel wrote:

...

Hi Doug,

I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 10/1/13 6:00 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

The way the software is set up, you should use mni152.register.dat
with
mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305)
surfaces

doug


On 10/01/2013 05:49 PM, Yang, Daniel wrote:

    Hi Doug,

    Just checking again, because I haven't heard from you. So the
    purpose
    is to use mri_vol2surf is convert MNI152 to a FreeSurfer
    (MNI305) mgh
    file. I am not sure about the correct register.dat to use. The
    mni152.register.dat is for MNI305 -> MNI152 though.

    I'm assuming that there exists some sort of inverse
    mni152.register.dat somewhere?

    Thanks!
    Daniel
    -- 
    Yung-Jui "Daniel" Yang, PhD
    Postdoctoral Researcher
    Yale Child Study Center
    New Haven, CT
    (203) 737-5454

    On 9/27/13 6:44 AM, "Yang, Daniel" <yung-jui.yang@yale.edu
    <mailto:yung-jui.yang@yale.edu>
    <mailto:yung-jui.yang@yale.edu>
    <mailto:yung-jui.yang@yale.edu%3E>> wrote:

         Thanks Doug!

         Because it maps from a MNI152 space to the FreeSurfer average
         space, do you know what register.dat I can use?

         Is it some sort of inverse mni152.register.dat?
         Thanks!
         Daniel

         --
         Yung-Jui "Daniel" Yang, PhD
         Postdoctoral Researcher
         Yale Child Study Center
         New Haven, CT
         (203) 737-5454

         On 9/26/13 12:26 PM, "Douglas N Greve"
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
         <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu%3E>> wrote:

             They might be sampling to different surfaces. To make
    sure
             they show the
             same exact thing, try mapping the data to the surface
    with
             mri_vol2surf
             doug
             On 09/25/2013 08:31 AM, Yang, Daniel wrote:

                 Dear FreeSurfer Experts,

                 I am trying to visualize fMRI activation
    (generated from
                 fsl) on the
                 fsaverage inflated surface, using
    mni152.register.dat.

                 It's odd that I find the results to be slightly
    different
                 between
                 tksurfer and freeview. However, I made sure that I am
                 using the same
                 threshold...

                 Judging from fslview, I think the result with
    freeview is
                 more
                 accurate -- is it due to tksurfer loading orig.mgz by
                 default, and
                 free view loading something else?

                 Thanks!
                 Daniel

                 --
                 Yung-Jui "Daniel" Yang, PhD
                 Postdoctoral Researcher
                 Yale Child Study Center
                 New Haven, CT
                 (203) 737-5454


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




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

Yang, Daniel

7:49 p.m.

Hi Doug,

I think I find out where the problem is. Actually the mri_vol2surf works nicely (and it's also true that tksurfer with -mni152reg samples the overlay to the white surface by default instead of to the pial surface.)

The problem is in freeview + rh.aparc.annot.

If you do the following for the attached rh mgh file, you will see it correctly displayed:

tksurfer fsaverage rh inflated -overlay rh.pial_surface.mni305.mgh

If you overlay this mgh in freeview with rh.inflated surface, but without loading rh.aparc.annot, it also displays correctly.

However, once I load the rh.aparc.annot, I start to see something very weird...

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 10/1/13 6:11 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

I don't understand what you mean by a "much smaller brain". Can you elaborate? On 10/01/2013 06:10 PM, Yang, Daniel wrote: Hi Doug,

I understand. But the end product turned out to be a much smaller brain … so I thought there is something wrong. What should I do here?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 10/1/13 6:00 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

The way the software is set up, you should use mni152.register.dat with mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces

doug

On 10/01/2013 05:49 PM, Yang, Daniel wrote:

Hi Doug,

I'm assuming that there exists some sort of inverse mni152.register.dat somewhere?

Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/27/13 6:44 AM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu%3E> wrote:

Thanks Doug!

Because it maps from a MNI152 space to the FreeSurfer average space, do you know what register.dat I can use?

Is it some sort of inverse mni152.register.dat? Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/26/13 12:26 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu%3E> wrote:

They might be sampling to different surfaces. To make sure they show the same exact thing, try mapping the data to the surface with mri_vol2surf doug On 09/25/2013 08:31 AM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold...

Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else?

Thanks! Daniel

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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

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Douglas N Greve
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