WM vol as measure

List overview All Threads
Download

newer

older

Re: [Freesurfer] Group Analysis...

Re: [Freesurfer] Freeview crashes...

Yang, Daniel

2 Mar 2014 2 Mar '14

7:18 p.m.

Dear FreeSurfer Experts,

FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor.

Thanks! Daniel

Show replies by date

Yang, Daniel

2 Mar 2 Mar

8:40 p.m.

Hi FreeSurfers,

A related question (I can't find the answers on the FS website): what's jacobian_white (as a measure)?

Thanks! Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/2/14 7:18 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:

Dear FreeSurfer Experts,

Thanks! Daniel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

Douglas N Greve

3 Mar 3 Mar

12:59 p.m.

That is the jacobian of the white matter surface when it is registered to fsaverage (not related to the actual white matter). On 03/02/2014 08:40 PM, Yang, Daniel wrote:

...

Hi FreeSurfers,

A related question (I can't find the answers on the FS website): what's jacobian_white (as a measure)?

Thanks! Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_

On 3/2/14 7:18 PM, "Yang, Daniel" <yung-jui.yang@yale.edu mailto:yung-jui.yang@yale.edu> wrote:
Dear FreeSurfer Experts,

FS provides thickness as the DV in qdec and mri-glmfit. Do you
know how I can have WM vol as the DV in these tools with the same
GLM model? For example, I want to test the WM regions that is most
strongly positively correlated with a given factor.

Thanks!
Daniel
_______________________________________________
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.
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

12:55 p.m.

Dear all,

I notice that there is a file called wmparc_stats.txt http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofwhi...

Is it possible to get corresponding WM info for a given label?

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/2/14 7:18 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:

Dear FreeSurfer Experts,

Douglas N Greve

12:58 p.m.

you can just add them into your qdec file (from wmparc.stats) doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote:

...

Dear FreeSurfer Experts,

FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor.

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

Yang, Daniel

1:07 p.m.

Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure).

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/3/14 12:58 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

you can just add them into your qdec file (from wmparc.stats) doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts,

-- 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/

_______________________________________________ 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

1:14 p.m.

It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote:

...

Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure).

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_

On 3/3/14 12:58 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

you can just add them into your qdec file (from wmparc.stats)
doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote:

    Dear FreeSurfer Experts,

    FS provides thickness as the DV in qdec and mri-glmfit. Do you
    know how I can have WM vol as the DV in these tools with the
    same GLM model? For example, I want to test the WM regions
    that is most strongly positively correlated with a given factor.

    Thanks!
    Daniel
    _______________________________________________
    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
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

2:12 p.m.

Hi Doug,

I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs.

However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)?

I'd like to use WM vol as DV but are limited to pre-defined ROIs.

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/3/14 1:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure).

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 3/3/14 12:58 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

you can just add them into your qdec file (from wmparc.stats) doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

-- 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

2:17 p.m.

I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under?

On 03/03/2014 02:12 PM, Yang, Daniel wrote:

...

Hi Doug,

I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs.

However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)?

I'd like to use WM vol as DV but are limited to pre-defined ROIs.

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_

On 3/3/14 1:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

It should be there if the recon did not fail. The file is called
wmparc.stats (not wmparc_stats.txt)
On 03/03/2014 01:07 PM, Yang, Daniel wrote:

    Thanks, Doug! But that is about using wmparc.stats as IV or
    continuous/covariate variables. I would like to use WM vol as
    the DV
    (measure).

    -- 
    Daniel (Yung-Jui) Yang, Ph.D.
    Postdoctoral Researcher
    Yale Child Study Center
    New Haven, CT
    Tel: (203) 737-5454
    E-mail: _yung-jui.yang@yale.edu_ <mailto:_yung-jui.yang@yale.edu_>

    On 3/3/14 12:58 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:

         you can just add them into your qdec file (from wmparc.stats)
         doug

         On 03/02/2014 07:18 PM, Yang, Daniel wrote:

             Dear FreeSurfer Experts,

             FS provides thickness as the DV in qdec and
    mri-glmfit. Do you
             know how I can have WM vol as the DV in these tools
    with the
             same GLM model? For example, I want to test the WM
    regions
             that is most strongly positively correlated with a
    given factor.

             Thanks!
             Daniel
    _______________________________________________
             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.



-- 
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/

Yang, Daniel

2:31 p.m.

Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface.

Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)?

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/3/14 2:17 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under?

On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug,

I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs.

However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)?

I'd like to use WM vol as DV but are limited to pre-defined ROIs.

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 3/3/14 1:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote:

Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure).

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_

you can just add them into your qdec file (from wmparc.stats) doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

Thanks! Daniel _______________________________________________ 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

Douglas N Greve

2:48 p.m.

yes, but not easily. You will have to create an annotation with your new label in it (and any other label for the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log file for example command lines for mri_aparc2aseg (used to generate the wmparc.mgz) doug On 03/03/2014 02:31 PM, Yang, Daniel wrote:

...

Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface.

Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)?

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_

On 3/3/14 2:17 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

I don't understand. What label do you have? Do you mean a WM label
or a
cortical label that you want to find the WM under?

On 03/03/2014 02:12 PM, Yang, Daniel wrote:

    Hi Doug,

    I am able to find wmparc.stats in stats. It shows WM vol based on
    pre-defined ROIs.

    However, do you know how can we generate corresponding WM vol
    for a
    given label (not the D-K ROIs)?

    I'd like to use WM vol as DV but are limited to pre-defined ROIs.

    Best,
    Daniel

    -- 
    Daniel (Yung-Jui) Yang, Ph.D.
    Postdoctoral Researcher
    Yale Child Study Center
    New Haven, CT
    Tel: (203) 737-5454
    E-mail: _yung-jui.yang@yale.edu_ <mailto:_yung-jui.yang@yale.edu_>

    On 3/3/14 1:14 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:

         It should be there if the recon did not fail. The file is
    called
         wmparc.stats (not wmparc_stats.txt)
         On 03/03/2014 01:07 PM, Yang, Daniel wrote:

             Thanks, Doug! But that is about using wmparc.stats as
    IV or
             continuous/covariate variables. I would like to use
    WM vol as
             the DV
             (measure).

             --
             Daniel (Yung-Jui) Yang, Ph.D.
             Postdoctoral Researcher
             Yale Child Study Center
             New Haven, CT
             Tel: (203) 737-5454
             E-mail: _yung-jui.yang@yale.edu_
    <mailto:_yung-jui.yang@yale.edu_>
    <mailto:_yung-jui.yang@yale.edu_>

             On 3/3/14 12:58 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>
             <mailto:greve@nmr.mgh.harvard.edu%3E>
    <mailto:greve@nmr.mgh.harvard.edu%3E%3E>> wrote:

                  you can just add them into your qdec file (from
    wmparc.stats)
                  doug

                  On 03/02/2014 07:18 PM, Yang, Daniel wrote:

                      Dear FreeSurfer Experts,

                      FS provides thickness as the DV in qdec and
             mri-glmfit. Do you
                      know how I can have WM vol as the DV in
    these tools
             with the
                      same GLM model? For example, I want to test
    the WM
             regions
                      that is most strongly positively correlated
    with a
             given factor.

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



         --
         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/



-- 
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/

Yang, Daniel

3:01 p.m.

Sounds like a lot of work, but thanks for your reply.

By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not necessarily the complete WM vol underneath the label?

Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/3/14 2:48 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)?

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 3/3/14 2:17 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under?

On 03/03/2014 02:12 PM, Yang, Daniel wrote:

Hi Doug,

I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs.

However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)?

I'd like to use WM vol as DV but are limited to pre-defined ROIs.

Best, Daniel

On 3/3/14 1:14 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:

It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote:

Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure).

On 3/3/14 12:58 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 mailto:greve@nmr.mgh.harvard.edu%3E mailto:greve@nmr.mgh.harvard.edu%3E%3E> wrote:

you can just add them into your qdec file (from wmparc.stats) doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

Thanks! Daniel _______________________________________________ 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

_______________________________________________ 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 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

3:35 p.m.

Right. How do you define the "complete WM vol underneath the label"?

On 03/03/2014 03:01 PM, Yang, Daniel wrote:

...

Sounds like a lot of work, but thanks for your reply.

By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not necessarily the complete WM vol underneath the label?

Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_

On 3/3/14 2:48 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

yes, but not easily. You will have to create an annotation with
your new
label in it (and any other label for the other parts of cortex)
(probably using mris_label2annot), then run mri_aparc2aseg to
generate a
new wmparc-style volume, then run mri_segstats. You can look in the
recon-all.log file for example command lines for mri_aparc2aseg
(used to
generate the wmparc.mgz)
doug
On 03/03/2014 02:31 PM, Yang, Daniel wrote:

    Sorry, I wasn't clear. It's a cortical label that I manually
    created,
    based on the pial surface.

    Is it possible to generate the corresponding WM vol based on a
    new
    label (not pre-defined)?


    -- 
    Daniel (Yung-Jui) Yang, Ph.D.
    Postdoctoral Researcher
    Yale Child Study Center
    New Haven, CT
    Tel: (203) 737-5454
    E-mail: _yung-jui.yang@yale.edu_ <mailto:_yung-jui.yang@yale.edu_>

    On 3/3/14 2:17 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:


         I don't understand. What label do you have? Do you mean a
    WM label
         or a
         cortical label that you want to find the WM under?

         On 03/03/2014 02:12 PM, Yang, Daniel wrote:

             Hi Doug,

             I am able to find wmparc.stats in stats. It shows WM
    vol based on
             pre-defined ROIs.

             However, do you know how can we generate
    corresponding WM vol
             for a
             given label (not the D-K ROIs)?

             I'd like to use WM vol as DV but are limited to
    pre-defined ROIs.

             Best,
             Daniel

             --
             Daniel (Yung-Jui) Yang, Ph.D.
             Postdoctoral Researcher
             Yale Child Study Center
             New Haven, CT
             Tel: (203) 737-5454
             E-mail: _yung-jui.yang@yale.edu_
    <mailto:_yung-jui.yang@yale.edu_>
    <mailto:_yung-jui.yang@yale.edu_>

             On 3/3/14 1:14 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>
             <mailto:greve@nmr.mgh.harvard.edu%3E>
    <mailto:greve@nmr.mgh.harvard.edu%3E%3E>> wrote:

                  It should be there if the recon did not fail.
    The file is
             called
                  wmparc.stats (not wmparc_stats.txt)
                  On 03/03/2014 01:07 PM, Yang, Daniel wrote:

                      Thanks, Doug! But that is about using
    wmparc.stats as
             IV or
                      continuous/covariate variables. I would like
    to use
             WM vol as
                      the DV
                      (measure).

                      --
                      Daniel (Yung-Jui) Yang, Ph.D.
                      Postdoctoral Researcher
                      Yale Child Study Center
                      New Haven, CT
                      Tel: (203) 737-5454
                      E-mail: _yung-jui.yang@yale.edu_
    <mailto:_yung-jui.yang@yale.edu_>
             <mailto:_yung-jui.yang@yale.edu_>
             <mailto:_yung-jui.yang@yale.edu_>

                      On 3/3/14 12:58 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>
                      <mailto:greve@nmr.mgh.harvard.edu>
                      <mailto:greve@nmr.mgh.harvard.edu%3E>
             <mailto:greve@nmr.mgh.harvard.edu%3E%3E>
    <mailto:greve@nmr.mgh.harvard.edu%3E%3E%3E>> wrote:

                           you can just add them into your qdec
    file (from
             wmparc.stats)
                           doug

                           On 03/02/2014 07:18 PM, Yang, Daniel wrote:

                               Dear FreeSurfer Experts,

                               FS provides thickness as the DV in
    qdec and
                      mri-glmfit. Do you
                               know how I can have WM vol as the DV in
             these tools
                      with the
                               same GLM model? For example, I want
    to test
             the WM
                      regions
                               that is most strongly positively
    correlated
             with a
                      given factor.

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



                  --
                  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>
             <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
    <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, 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/



-- 
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/

Yang, Daniel

4 p.m.

I can't either. But I am wondering if it is possible to calculate some thing like "distance from center of the brain to the white surface"? it is like cortical thickness but can be called white matter thickness/depth??

I want to see if WM expands over time in some regions versus other regions…

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/3/14 3:35 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

Right. How do you define the "complete WM vol underneath the label"?

On 03/03/2014 03:01 PM, Yang, Daniel wrote: Sounds like a lot of work, but thanks for your reply.

By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not necessarily the complete WM vol underneath the label?

Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 3/3/14 2:48 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface.

Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)?

On 3/3/14 2:17 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:

I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under?

On 03/03/2014 02:12 PM, Yang, Daniel wrote:

Hi Doug,

I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs.

However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)?

I'd like to use WM vol as DV but are limited to pre-defined ROIs.

Best, Daniel

It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote:

Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure).

you can just add them into your qdec file (from wmparc.stats) doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

Thanks! Daniel _______________________________________________ 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 mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ 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 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

4477

Age (days ago)

4477

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

13 comments

2 participants

tags (0)

participants (2)

Douglas N Greve
Yang, Daniel