functional ROI-based structural statistics?

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Re: [Freesurfer] Fwd: infant atlas...

Yang, Daniel

6 Aug 2013 6 Aug '13

12:18 a.m.

Dear FreeSurfer Experts,

Theoretically, if you have a set of functional ROIs, is it possible to derive the cortical thickness, white surface area, and gray matter volume of those functional ROIs in FreeSurfer?

Many thanks!! Daniel

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

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Bruce Fischl

6 Aug 6 Aug

9:33 a.m.

yes, if they are surface-based then it is really trivial (just give them to mris_anatomical_stats with the -l <label name> flag)

cheers Bruce

On Tue, 6 Aug 2013, Yang, Daniel wrote:

...

Dear FreeSurfer Experts,

Theoretically, if you have a set of functional ROIs, is it possible to derive the cortical thickness, white surface area, and gray matter volume of those functional ROIs in FreeSurfer?

Many thanks!! Daniel

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

Yang, Daniel

10 a.m.

Hi Bruce,

Thanks for your reply. Those functional ROIs are volume-based (that is, generated by spm/fsl/BrainVoyager).

So it seems that I need to generate a label for them in order to use mris_anatomical_stats -l.

Do you know what I can generate label files based on volumetric functional ROIs? I'm also a little bit puzzled because a given functional ROI may not capture the whole gray matter within a certain region, how can we determine its volume/area/thickness?

Many thanks! Daniel

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

On 8/6/13 9:33 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

yes, if they are surface-based then it is really trivial (just give them to mris_anatomical_stats with the -l <label name> flag)

cheers Bruce

On Tue, 6 Aug 2013, Yang, Daniel wrote:

Dear FreeSurfer Experts, Theoretically, if you have a set of functional ROIs, is it possible to derive the cortical thickness, white surface area, and gray matter volume of those functional ROIs in FreeSurfer? Many thanks!! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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.

Douglas N Greve

2:28 p.m.

Register your fMRI to the anatomical, sample the ROIs from the fMRI space to the surface, display in tksurfer, create and save the labels you want, then run mri_segstats using the label and thickness as input.

doug

On 08/06/2013 10:00 AM, Yang, Daniel wrote:

...

Hi Bruce,

Thanks for your reply. Those functional ROIs are volume-based (that is, generated by spm/fsl/BrainVoyager).

So it seems that I need to generate a label for them in order to use mris_anatomical_stats -l.

Do you know what I can generate label files based on volumetric functional ROIs? I'm also a little bit puzzled because a given functional ROI may not capture the whole gray matter within a certain region, how can we determine its volume/area/thickness?

Many thanks! Daniel

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

On 8/6/13 9:33 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
yes, if they are surface-based then it is really trivial (just
give them to
mris_anatomical_stats with the -l <label name> flag)

cheers
Bruce


On Tue, 6 Aug 2013, Yang, Daniel wrote:

    Dear FreeSurfer Experts,
    Theoretically, if you have a set of functional ROIs, is it
    possible to
    derive the cortical thickness, white surface area, and gray
    matter volume of
    those functional ROIs in FreeSurfer?
    Many thanks!!
    Daniel
    -- 
    Yung-Jui "Daniel" Yang, PhD
    Postdoctoral Researcher
    Yale Child Study Center
    New Haven, CT
    (203) 737-5454



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

-- 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

2:49 p.m.

Thanks, Doug, for the procedure. I'm just wondering how the ROI sampling is performed.

May I ask three questions?

(a) when you say sample the ROIs from the fMRI space to the "surface", are you referring to white or pial surface?

(b) Let's say, the functional activation is halfway inside a certain region and closer down to the white surface (that is, the gray matter near the pial surface is not significantly activated, while the gray matter near the white surface is activated). When the program samples this ROI to a "surface", does it basically do a maximum intensity projection to the pial surface? that is, underneath certain pial/cortical surface, there exists a functional activation?

(c) if the activation is partially inside the white matter, how would the sampling program deal with it? would it just ignore the part within the white matter?

Thanks, Daniel

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

On 8/6/13 2:28 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

doug

On 08/06/2013 10:00 AM, Yang, Daniel wrote: Hi Bruce,

Thanks for your reply. Those functional ROIs are volume-based (that is, generated by spm/fsl/BrainVoyager).

So it seems that I need to generate a label for them in order to use mris_anatomical_stats -l.

Many thanks! Daniel

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

On 8/6/13 9:33 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

yes, if they are surface-based then it is really trivial (just give them to mris_anatomical_stats with the -l <label name> flag)

cheers Bruce

On Tue, 6 Aug 2013, Yang, Daniel wrote:

_______________________________________________ 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/

Douglas N Greve

2:55 p.m.

On 08/06/2013 02:49 PM, Yang, Daniel wrote:

...

Thanks, Doug, for the procedure. I'm just wondering how the ROI sampling is performed.

May I ask three questions?

(a) when you say sample the ROIs from the fMRI space to the "surface", are you referring to white or pial surface?

You can have it fill the ribbon or sample the maximum. see the --help

...

(b) Let's say, the functional activation is halfway inside a certain region and closer down to the white surface (that is, the gray matter near the pial surface is not significantly activated, while the gray matter near the white surface is activated). When the program samples this ROI to a "surface", does it basically do a maximum intensity projection to the pial surface? that is, underneath certain pial/cortical surface, there exists a functional activation?

You can do it a bunch of different ways, including max intensity projection over the ribbon.

...

(c) if the activation is partially inside the white matter, how would the sampling program deal with it? would it just ignore the part within the white matter?

You can give it a negative start to the projection fraction and it will sample in the WM. doug

...

Thanks, Daniel

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

On 8/6/13 2:28 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Register your fMRI to the anatomical, sample the ROIs from the fMRI
space to the surface, display in tksurfer, create and save the labels
you want, then run mri_segstats using the label and thickness as
input.

doug

On 08/06/2013 10:00 AM, Yang, Daniel wrote:

    Hi Bruce,

    Thanks for your reply. Those functional ROIs are volume-based
    (that
    is, generated by spm/fsl/BrainVoyager).

    So it seems that I need to generate a label for them in order to
    use mris_anatomical_stats -l.

    Do you know what I can generate label files based on volumetric
    functional ROIs? I'm also a little bit puzzled because a given
    functional ROI may not capture the whole gray matter within a
    certain
    region, how can we determine its volume/area/thickness?

    Many thanks!
    Daniel

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

    On 8/6/13 9:33 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>
    <mailto:fischl@nmr.mgh.harvard.edu>
    <mailto:fischl@nmr.mgh.harvard.edu%3E>> wrote:

         yes, if they are surface-based then it is really trivial
    (just
         give them to
         mris_anatomical_stats with the -l <label name> flag)

         cheers
         Bruce


         On Tue, 6 Aug 2013, Yang, Daniel wrote:

             Dear FreeSurfer Experts,
             Theoretically, if you have a set of functional ROIs,
    is it
             possible to
             derive the cortical thickness, white surface area,
    and gray
             matter volume of
             those functional ROIs in FreeSurfer?
             Many thanks!!
             Daniel
             --
             Yung-Jui "Daniel" Yang, PhD
             Postdoctoral Researcher
             Yale Child Study Center
             New Haven, CT
             (203) 737-5454



         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
    <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

4:09 p.m.

Hi Doug,

So the program to be used is mri_vol2surf, correct? Is there any other program that might be related?

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

On 8/6/13 2:55 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

On 08/06/2013 02:49 PM, Yang, Daniel wrote: Thanks, Doug, for the procedure. I'm just wondering how the ROI sampling is performed.

May I ask three questions?

(a) when you say sample the ROIs from the fMRI space to the "surface", are you referring to white or pial surface? You can have it fill the ribbon or sample the maximum. see the --help

(c) if the activation is partially inside the white matter, how would the sampling program deal with it? would it just ignore the part within the white matter? You can give it a negative start to the projection fraction and it will sample in the WM. doug

Thanks, Daniel

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

On 8/6/13 2:28 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

doug

On 08/06/2013 10:00 AM, Yang, Daniel wrote:

Hi Bruce,

Thanks for your reply. Those functional ROIs are volume-based (that is, generated by spm/fsl/BrainVoyager).

So it seems that I need to generate a label for them in order to use mris_anatomical_stats -l.

Many thanks! Daniel

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

On 8/6/13 9:33 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu%3E> wrote:

yes, if they are surface-based then it is really trivial (just give them to mris_anatomical_stats with the -l <label name> flag)

cheers Bruce

On Tue, 6 Aug 2013, Yang, Daniel wrote:

_______________________________________________ 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

4:11 p.m.

yes, mri_vol2surf. no other program that I know of doug On 08/06/2013 04:09 PM, Yang, Daniel wrote:

...

Hi Doug,

So the program to be used is mri_vol2surf, correct? Is there any other program that might be related?

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

On 8/6/13 2:55 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

On 08/06/2013 02:49 PM, Yang, Daniel wrote:

    Thanks, Doug, for the procedure. I'm just wondering how the ROI
    sampling is performed.

    May I ask three questions?

    (a) when you say sample the ROIs from the fMRI space to the
    "surface",
    are you referring to white or pial surface?

You can have it fill the ribbon or sample the maximum. see the --help


    (b) Let's say, the functional activation is halfway inside a
    certain
    region and closer down to the white surface (that is, the gray
    matter
    near the pial surface is not significantly activated, while
    the gray
    matter near the white surface is activated). When the program
    samples
    this ROI to a "surface", does it basically do a maximum intensity
    projection to the pial surface? that is, underneath certain
    pial/cortical surface, there exists a functional activation?

You can do it a bunch of different ways, including max intensity
projection over the ribbon.


    (c) if the activation is partially inside the white matter,
    how would
    the sampling program deal with it? would it just ignore the part
    within the white matter?

You can give it a negative start to the projection fraction and it
will
sample in the WM.
doug


    Thanks,
    Daniel

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

    On 8/6/13 2:28 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:

         Register your fMRI to the anatomical, sample the ROIs
    from the fMRI
         space to the surface, display in tksurfer, create and
    save the labels
         you want, then run mri_segstats using the label and
    thickness as
         input.

         doug

         On 08/06/2013 10:00 AM, Yang, Daniel wrote:

             Hi Bruce,

             Thanks for your reply. Those functional ROIs are
    volume-based
             (that
             is, generated by spm/fsl/BrainVoyager).

             So it seems that I need to generate a label for them
    in order to
             use mris_anatomical_stats -l.

             Do you know what I can generate label files based on
    volumetric
             functional ROIs? I'm also a little bit puzzled
    because a given
             functional ROI may not capture the whole gray matter
    within a
             certain
             region, how can we determine its volume/area/thickness?

             Many thanks!
             Daniel

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

             On 8/6/13 9:33 AM, "Bruce Fischl"
    <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>
             <mailto:fischl@nmr.mgh.harvard.edu>
             <mailto:fischl@nmr.mgh.harvard.edu>
             <mailto:fischl@nmr.mgh.harvard.edu%3E>
    <mailto:fischl@nmr.mgh.harvard.edu%3E%3E>> wrote:

                  yes, if they are surface-based then it is really
    trivial
             (just
                  give them to
                  mris_anatomical_stats with the -l <label name> flag)

                  cheers
                  Bruce


                  On Tue, 6 Aug 2013, Yang, Daniel wrote:

                      Dear FreeSurfer Experts,
                      Theoretically, if you have a set of
    functional ROIs,
             is it
                      possible to
                      derive the cortical thickness, white surface
    area,
             and gray
                      matter volume of
                      those functional ROIs in FreeSurfer?
                      Many thanks!!
                      Daniel
                      --
                      Yung-Jui "Daniel" Yang, PhD
                      Postdoctoral Researcher
                      Yale Child Study Center
                      New Haven, CT
                      (203) 737-5454



                  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
    <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


-- 
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/

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Bruce Fischl
Douglas N Greve
Yang, Daniel