Cortical gray matter surface area

List overview All Threads
Download

newer

older

Postdoctoral position at...

fsfast: using an empirically...

will brown

1 Sep 2014 1 Sep '14

6:22 p.m.

Hi all,

I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.

?.aparc.stats reports:

Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2

How about the gray matter?

Thanks, Will

Attachments:

attachment.html (text/html — 910 bytes)

Show replies by date

Krieger, Donald N.

1 Sep 1 Sep

6:29 p.m.

Hi Will,

I think lh.ribbon.mgz and lh.ribbon.mgz contain the volumes of the left and right cortical gray matter. You can extract a list of vectors on a 1 mm grid which fills these regions using mri_cor2label and count the vectors.

Regards,

Don

Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of will brown Sent: Monday, September 01, 2014 6:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cortical gray matter surface area

Hi all,

I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.

?.aparc.stats reports:

Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2

How about the gray matter?

Thanks, Will

_andreia_＠sapo.pt

2 Sep 2 Sep

9:12 a.m.

Hi Will,

I use the following commands to get surface area from the pial surface:

In the subject label dir:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial

mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.APARC.PIAL.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial

Then run aparcstats2table using APARC.PIAL instead of aparc (only because I called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:

mris_anatomical_stats -l ../label/lh.cortex.label -f lh.TOTAL_PIAL.stats -b SUBJ lh pial

mris_anatomical_stats -l ../label/rh.cortex.label -f rh.TOTAL_PIAL.stats -b SUBJ rh pial

Then run aparcstats2table using TOTAL_PIAL instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)

Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best, Andreia

Citando will brown willbrown1987@gmail.com:

...

Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2 How about the gray matter? Thanks, Will

will brown

9 Sep 9 Sep

1:36 a.m.

Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary.

Will

On Wed, Sep 3, 2014 at 1:12 AM, _andreia_@sapo.pt wrote:

...

Hi Will,

I use the following commands to get surface area from the pial surface:

In the subject label dir:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh. *aparc.pial*.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial

mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh. *aparc.pial*.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial

Then run aparcstats2table using *aparc.pial* instead of aparc (only because I called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:

mris_anatomical_stats -l ../label/lh.cortex.label -f lh.*total_pial*.stats -b SUBJ lh pial

mris_anatomical_stats -l ../label/rh.cortex.label -f rh.*total_pial*.stats -b SUBJ rh pial

Then run aparcstats2table using *total_pial* instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)

Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best, Andreia

Citando will brown willbrown1987@gmail.com:

Hi all,

I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.

?.aparc.stats reports:

Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2

How about the gray matter?

Thanks, Will

will brown

5:43 a.m.

Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things;

1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex?

2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: *# Measure Cortex, WhiteSurfArea, White Surface Total Area,* ?

Thanks again, Will

On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1987@gmail.com wrote:

...

Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary.

Will

On Wed, Sep 3, 2014 at 1:12 AM, _andreia_@sapo.pt wrote:

...
Hi Will,

I use the following commands to get surface area from the pial surface:

In the subject label dir:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.*aparc.pial*.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial

mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.*aparc.pial*.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial

Then run aparcstats2table using *aparc.pial* instead of aparc (only because I called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:

mris_anatomical_stats -l ../label/lh.cortex.label -f lh.*total_pial*.stats -b SUBJ lh pial

mris_anatomical_stats -l ../label/rh.cortex.label -f rh.*total_pial*.stats -b SUBJ rh pial

Then run aparcstats2table using *total_pial* instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)

Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best, Andreia

Citando will brown willbrown1987@gmail.com:

Hi all,

I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.

?.aparc.stats reports:

Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2

How about the gray matter?

Thanks, Will

_andreia_＠sapo.pt

7 a.m.

Hi Will,

Just to clarify, what version of FS are you using? I think it might not be 5.0 and I don't know if everything aplies if we are using different versions.

1) Yes, it is only based on the pial surface (and these command lines are for the aparc, DK altas). The second set provides the surface area for each hemisphere without including, for example, the pial surface that you see in the hippocampus which is not accurate and one should not care about. In the end, the second set gives you the sum of the areas in aparc, thus, you can just make a sum of that parcellation if you want. I just realized that.

2) No. In the new stats file, the value that you want is at the bottom:

# ColHeaders StructName NumVert SURFAREA GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

And when running aparcstats2table that's the value you should get in the table. I think that # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA may be including more stuff since it is bigger.

If what you want is only the total hemisphere surface area you only need to run the second set of commands. If you want the area of each DK altas parcellation then run the first set and then simply add them to get total hemisphere surface area.

Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm Ccing Doug since he was replying to your previous emails.

Let's wait for their feedback.

Andreia

Citando will brown willbrown1987@gmail.com:

...

Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things;

The first commands you have given provide the stats for the two

hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? 2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA, ? Thanks again, Will

On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1987@gmail.com wrote:

...
Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will
    On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt> wrote:
...
_Hi Will,

I use the following commands to get surface area from the pial surface:

In the subject label dir:_
       _mris_anatomical_stats -mgz -cortex
../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial_
       _mris_anatomical_stats -mgz -cortex
../label/rh.cortex.label -f ../stats/rh.APARC.PIAL.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial _

_Then run aparcstats2table using APARC.PIAL instead of aparc (only because I called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:_
       _mris_anatomical_stats -l ../label/lh.cortex.label -f
lh.TOTAL_PIAL.stats -b SUBJ lh pial_
       _mris_anatomical_stats -l ../label/rh.cortex.label -f
rh.TOTAL_PIAL.stats -b SUBJ rh pial_
       _Then run aparcstats2table using TOTAL_PIAL instead of
aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)_

_Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best, Andreia_
       _Citando will brown <willbrown1987@gmail.com>:_
...
_Hi all, _ _ _ _I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info._ _ _ _?.aparc.stats reports:_ _ _ _Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2_ _ _ _How about the gray matter?_ _ _ _Thanks,_ _Will_ _ _ _ _

_ _

will brown

11 Sep 11 Sep

2:24 a.m.

Thanks again, for the record, I'm using freesurfer version 5.3.0 on Centos 6. On 9/09/2014 11:00 PM, _andreia_@sapo.pt wrote:

...

Hi Will,

Just to clarify, what version of FS are you using? I think it might not be 5.0 and I don't know if everything aplies if we are using different versions.

Yes, it is only based on the pial surface (and these command lines are

for the aparc, DK altas). The second set provides the surface area for each hemisphere without including, for example, the pial surface that you see in the hippocampus which is not accurate and one should not care about. In the end, the second set gives you the sum of the areas in aparc, thus, you can just make a sum of that parcellation if you want. I just realized that.

No. In the new stats file, the value that you want is at the bottom:

# ColHeaders StructName NumVert *SurfArea* GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

And when running aparcstats2table that's the value you should get in the table. I think that *# Measure Cortex, WhiteSurfArea, White Surface Total Area* may be including more stuff since it is bigger.

If what you want is only the total hemisphere surface area you only need to run the second set of commands. If you want the area of each DK altas parcellation then run the first set and then simply add them to get total hemisphere surface area.

Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm Ccing Doug since he was replying to your previous emails.

Let's wait for their feedback.

Andreia

Citando will brown willbrown1987@gmail.com:

Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things;

The first commands you have given provide the stats for the two

hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex?

The surface area value that I am looking for (grey matter surface area

at the grey/pial boundary) is listed in the new stats table next to: *# Measure Cortex, WhiteSurfArea, White Surface Total Area,* ?

Thanks again, Will

On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1987@gmail.com wrote:

...
Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary.

Will

On Wed, Sep 3, 2014 at 1:12 AM, _andreia_@sapo.pt wrote:

...
*Hi Will, I use the following commands to get surface area from the pial surface: In the subject label dir:*

*mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial*

*mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial *

*Then run aparcstats2table using aparc.pial instead of aparc (only because I called this new parcellation aparc.pial) To get the total surface area of each hemisphere I use: In the subject stats dir:*

*mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total_pial.stats -b SUBJ lh pial*

*mris_anatomical_stats -l ../label/rh.cortex.label -f rh.total_pial.stats -b SUBJ rh pial*

*Then run aparcstats2table using total_pial instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)*

*Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir. I use FS 5.0. Is this what you want? Best, Andreia*

*Citando will brown <willbrown1987@gmail.com willbrown1987@gmail.com>:*

*Hi all,*

*I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.*

*?.aparc.stats reports:*

*Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2*

*How about the gray matter?*

*Thanks,* *Will*

_andreia_＠sapo.pt

2:29 p.m.

Ok. Then, I'm not sure if everything is correct with the command lines since I use 5.0.

Any thought on this Freesurfer team?

Thanks, Andreia

Citando will brown willbrown1987@gmail.com:

...

Thanks again, for the record, I'm using freesurfer version 5.3.0 on Centos 6. On 9/09/2014 11:00 PM, _andreia_@sapo.pt wrote:

...
_Hi Will,

Just to clarify, what version of FS are you using? I think it might not be 5.0 and I don't know if everything aplies if we are using different versions.

Yes, it is only based on the pial surface (and these command lines

are for the aparc, DK altas). The second set provides the surface area for each hemisphere without including, for example, the pial surface that you see in the hippocampus which is not accurate and one should not care about. In the end, the second set gives you the sum of the areas in aparc, thus, you can just make a sum of that parcellation if you want. I just realized that.

No. In the new stats file, the value that you want is at the bottom:

# ColHeaders StructName NumVert SURFAREA GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

And when running aparcstats2table that's the value you should get in the table. I think that # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA may be including more stuff since it is bigger.

If what you want is only the total hemisphere surface area you only need to run the second set of commands. If you want the area of each DK altas parcellation then run the first set and then simply add them to get total hemisphere surface area.

Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm Ccing Doug since he was replying to your previous emails.

Let's wait for their feedback.

Andreia_
 _Citando will brown <willbrown1987@gmail.com>:_
...
_Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things; _ _1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? _ _2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA, ? _ _Thanks again, Will_
   _On Tue, Sep 9, 2014 at 5:36 PM, will brown
willbrown1987@gmail.com wrote:_

...
_Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. _ _ _ _Will_
        _On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt>
wrote:_

...
__Hi Will,

I use the following commands to get surface area from the pial surface:

In the subject label dir:_ _
           __mris_anatomical_stats -mgz -cortex
../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial__
           __mris_anatomical_stats -mgz -cortex
../label/rh.cortex.label -f ../stats/rh.APARC.PIAL.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial __

__Then run aparcstats2table using APARC.PIAL instead of aparc (only because I called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:_ _
           __mris_anatomical_stats -l ../label/lh.cortex.label
-f lh.TOTAL_PIAL.stats -b SUBJ lh pial__
           __mris_anatomical_stats -l ../label/rh.cortex.label
-f rh.TOTAL_PIAL.stats -b SUBJ rh pial__
           __Then run aparcstats2table using TOTAL_PIAL instead
of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)__

__Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best, Andreia_

_
           __Citando will brown <willbrown1987@gmail.com>:__
...
__Hi all,_ _ __ __ __I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.__ __ __ __?.aparc.stats reports:__ __ __ __Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2__ __ __ __How about the gray matter?__ __ __ __Thanks,__ __Will__ __ __ __ __

_ _ __ __
_ _

Bruce Fischl

5:11 p.m.

sorry, this thread has gotten too deep. Can someone summarize the question?

On Thu, 11 Sep 2014, _andreia_@sapo.pt wrote:

...

Ok. Then, I'm not sure if everything is correct with the command lines since I use 5.0.

Any thought on this Freesurfer team?

Thanks, Andreia

Citando will brown willbrown1987@gmail.com:

  Thanks again, for the record, I'm using freesurfer version 5.3.0
  on Centos 6.

  On 9/09/2014 11:00 PM, <_andreia_@sapo.pt> wrote:

        Hi Will,

        Just to clarify, what version of FS are you using? I
        think it might not be 5.0 and I don't know if
        everything aplies if we are using different
        versions.


        1) Yes, it is only based on the pial surface (and
        these command lines are for the aparc, DK altas).
        The second set provides the surface area for each
        hemisphere without including, for example, the pial
        surface that you see in the hippocampus which is not
        accurate and one should not care about. In the end,
        the second set gives you the sum of the areas in
        aparc, thus, you can just make a sum of that
        parcellation if you want. I just realized that.

        2) No. In the new stats file, the value that you
        want is at the bottom:

        # ColHeaders StructName NumVert SurfArea GrayVol
        ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

        And when running aparcstats2table that's the value
        you should get in the table. I think that # Measure
        Cortex, WhiteSurfArea, White Surface Total Area may
        be including more stuff since it is bigger.


        If what you want is only the total hemisphere
        surface area you only need to run the second set of
        commands. If you want the area of each DK altas
        parcellation then run the first set and then simply
        add them to get total hemisphere surface area.


        Someone from Freesurfer staff will correct me if I'm
        wrong. (Please) I'm Ccing Doug since he was replying
        to your previous emails.

        Let's wait for their feedback.

        Andreia



         

        Citando will brown <willbrown1987@gmail.com>:

              Thanks Andreia, this does appear to have
              worked. Please forgive my ignorance but
              I do just want to double check two
              things;

The first commands you have given provide the stats for

the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? 2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: # Measure Cortex, WhiteSurfArea, White Surface Total Area, ? Thanks again, Will

On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1987@gmail.com wrote: Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will

On Wed, Sep 3, 2014 at 1:12 AM, _andreia_@sapo.pt wrote:

  Hi Will,

  I use the following commands to get
  surface area from the pial surface:


  In the subject label dir:
   

  mris_anatomical_stats -mgz -cortex
  ../label/lh.cortex.label -f
  ../stats/lh.aparc.pial.stats -b -a
  ../label/lh.aparc.annot -c
  ../label/aparc.annot.ctab SUBJ lh pial

  mris_anatomical_stats -mgz -cortex
  ../label/rh.cortex.label -f
  ../stats/rh.aparc.pial.stats -b -a
  ../label/rh.aparc.annot -c
  ../label/aparc.annot.ctab SUBJ rh pial
   


  Then run aparcstats2table using
  aparc.pial instead of aparc (only
  because I called this new parcellation
  aparc.pial)



  To get the total surface area of each
  hemisphere I use:

  In the subject stats dir:
   

  mris_anatomical_stats -l
  ../label/lh.cortex.label -f
  lh.total_pial.stats -b SUBJ lh pial

  mris_anatomical_stats -l
  ../label/rh.cortex.label -f
  rh.total_pial.stats -b SUBJ rh pial

  Then run aparcstats2table using
  total_pial instead of aparc (again, only
  because I called this new parcellation
  total_pial. You may call it whatever
  you'd like)



  Just remeber to leave the specified dirs
  when creating the tables. If you dont't
  I think they will be created in the
  current dir.

  I use FS 5.0.

  Is this what you want?


  Best,
  Andreia

   

  Citando will brown
  <willbrown1987@gmail.com>:

        Hi all,

I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2 How about the gray matter? Thanks, Will

will brown

7:29 p.m.

Sure. We'd like to know how to find the surface area of the cortical grey matter from the pial surface. So specifically, what is the surface area of the pial/grey matter boundary of the cortex for each hemisphere?

We're using Freesurfer v5.3 on Centos 6.

Thanks, Will Brown

On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

sorry, this thread has gotten too deep. Can someone summarize the question?

On Thu, 11 Sep 2014, _andreia_@sapo.pt wrote:

...
Ok. Then, I'm not sure if everything is correct with the command lines since I use 5.0.

Any thought on this Freesurfer team?

Thanks, Andreia

Citando will brown willbrown1987@gmail.com:
  Thanks again, for the record, I'm using freesurfer version 5.3.0
  on Centos 6.

  On 9/09/2014 11:00 PM, <_andreia_@sapo.pt> wrote:

        Hi Will,

        Just to clarify, what version of FS are you using? I
        think it might not be 5.0 and I don't know if
        everything aplies if we are using different
        versions.


        1) Yes, it is only based on the pial surface (and
        these command lines are for the aparc, DK altas).
        The second set provides the surface area for each
        hemisphere without including, for example, the pial
        surface that you see in the hippocampus which is not
        accurate and one should not care about. In the end,
        the second set gives you the sum of the areas in
        aparc, thus, you can just make a sum of that
        parcellation if you want. I just realized that.

        2) No. In the new stats file, the value that you
        want is at the bottom:

        # ColHeaders StructName NumVert SurfArea GrayVol
        ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

        And when running aparcstats2table that's the value
        you should get in the table. I think that # Measure
        Cortex, WhiteSurfArea, White Surface Total Area may
        be including more stuff since it is bigger.


        If what you want is only the total hemisphere
        surface area you only need to run the second set of
        commands. If you want the area of each DK altas
        parcellation then run the first set and then simply
        add them to get total hemisphere surface area.


        Someone from Freesurfer staff will correct me if I'm
        wrong. (Please) I'm Ccing Doug since he was replying
        to your previous emails.

        Let's wait for their feedback.

        Andreia





        Citando will brown <willbrown1987@gmail.com>:

              Thanks Andreia, this does appear to have
              worked. Please forgive my ignorance but
              I do just want to double check two
              things;
The first commands you have given provide the stats for

the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex?

The surface area value that I am looking for (grey

matter surface area at the grey/pial boundary) is listed in the new stats table next to: # Measure Cortex, WhiteSurfArea, White Surface Total Area, ?

Thanks again, Will

On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1987@gmail.com wrote: Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will

On Wed, Sep 3, 2014 at 1:12 AM, _andreia_@sapo.pt wrote:
  Hi Will,

  I use the following commands to get
  surface area from the pial surface:


  In the subject label dir:


  mris_anatomical_stats -mgz -cortex
  ../label/lh.cortex.label -f
  ../stats/lh.aparc.pial.stats -b -a
  ../label/lh.aparc.annot -c
  ../label/aparc.annot.ctab SUBJ lh pial

  mris_anatomical_stats -mgz -cortex
  ../label/rh.cortex.label -f
  ../stats/rh.aparc.pial.stats -b -a
  ../label/rh.aparc.annot -c
  ../label/aparc.annot.ctab SUBJ rh pial



  Then run aparcstats2table using
  aparc.pial instead of aparc (only
  because I called this new parcellation
  aparc.pial)



  To get the total surface area of each
  hemisphere I use:

  In the subject stats dir:


  mris_anatomical_stats -l
  ../label/lh.cortex.label -f
  lh.total_pial.stats -b SUBJ lh pial

  mris_anatomical_stats -l
  ../label/rh.cortex.label -f
  rh.total_pial.stats -b SUBJ rh pial

  Then run aparcstats2table using
  total_pial instead of aparc (again, only
  because I called this new parcellation
  total_pial. You may call it whatever
  you'd like)



  Just remeber to leave the specified dirs
  when creating the tables. If you dont't
  I think they will be created in the
  current dir.

  I use FS 5.0.

  Is this what you want?


  Best,
  Andreia



  Citando will brown
  <willbrown1987@gmail.com>:

        Hi all,
I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.

?.aparc.stats reports:

Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2

How about the gray matter?

Thanks, Will
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

12 Sep 12 Sep

11:27 a.m.

You can run something like

cd $SUBJECTS_DIR/subject

mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab subject lh pial

The "Measure Cortex" fields in the output stats/lh.aparc.pial.stats will be measures of the pial surface as will the SurfArea, MeanCurv, GausCurv, FoldInd, and CurvInd fields for each ROI (thickness and number of vertices will stay the same)

doug

On 09/11/2014 07:29 PM, will brown wrote:

...

We're using Freesurfer v5.3 on Centos 6.

Thanks, Will Brown

On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

sorry, this thread has gotten too deep. Can someone summarize the
question?


On Thu, 11 Sep 2014, _andreia_@sapo.pt <mailto:andreia_@sapo.pt>
wrote:


    Ok. Then, I'm not sure if everything is correct with the
    command lines since
    I use 5.0.

    Any thought on this Freesurfer team?

    Thanks,
    Andreia

    Citando will brown <willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>:

          Thanks again, for the record, I'm using freesurfer
    version 5.3.0
          on Centos 6.

          On 9/09/2014 11:00 PM, <_andreia_@sapo.pt
    <mailto:andreia_@sapo.pt>> wrote:

                Hi Will,

                Just to clarify, what version of FS are you using? I
                think it might not be 5.0 and I don't know if
                everything aplies if we are using different
                versions.


                1) Yes, it is only based on the pial surface (and
                these command lines are for the aparc, DK altas).
                The second set provides the surface area for each
                hemisphere without including, for example, the pial
                surface that you see in the hippocampus which is not
                accurate and one should not care about. In the end,
                the second set gives you the sum of the areas in
                aparc, thus, you can just make a sum of that
                parcellation if you want. I just realized that.

                2) No. In the new stats file, the value that you
                want is at the bottom:

                # ColHeaders StructName NumVert SurfArea GrayVol
                ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

                And when running aparcstats2table that's the value
                you should get in the table. I think that # Measure
                Cortex, WhiteSurfArea, White Surface Total Area may
                be including more stuff since it is bigger.


                If what you want is only the total hemisphere
                surface area you only need to run the second set of
                commands. If you want the area of each DK altas
                parcellation then run the first set and then simply
                add them to get total hemisphere surface area.


                Someone from Freesurfer staff will correct me if I'm
                wrong. (Please) I'm Ccing Doug since he was replying
                to your previous emails.

                Let's wait for their feedback.

                Andreia





                Citando will brown <willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>:

                      Thanks Andreia, this does appear to have
                      worked. Please forgive my ignorance but
                      I do just want to double check two
                      things;

    1) The first commands you have given provide the stats for
    the two hemispheres of the cerebral cortex only based on
    the pial surface, whereas the second set of commands
    provide the pial boundary stats for the whole brain rather
    than just cortex?

    2) The surface area value that I am looking for (grey
    matter surface area at the grey/pial boundary) is listed
    in the new stats table next to: # Measure Cortex,
    WhiteSurfArea, White Surface Total Area, ?

    Thanks again,
    Will

    On Tue, Sep 9, 2014 at 5:36 PM, will brown
    <willbrown1987@gmail.com <mailto:willbrown1987@gmail.com>> wrote:
          Thanks very much Andreia, yes this does look
          like what I want. I haven't had a chance to
          test it yet but it does indeed appear to
          answer my question. Thanks to those that have
          offered answers, to clarify, I did indeed mean
          the surface area of the pial surface rather
          than the white/grey boundary.
    Will


    On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt
    <mailto:andreia_@sapo.pt>>
    wrote:

          Hi Will,

          I use the following commands to get
          surface area from the pial surface:


          In the subject label dir:


          mris_anatomical_stats -mgz -cortex
          ../label/lh.cortex.label -f
          ../stats/lh.aparc.pial.stats -b -a
          ../label/lh.aparc.annot -c
          ../label/aparc.annot.ctab SUBJ lh pial

          mris_anatomical_stats -mgz -cortex
          ../label/rh.cortex.label -f
          ../stats/rh.aparc.pial.stats -b -a
          ../label/rh.aparc.annot -c
          ../label/aparc.annot.ctab SUBJ rh pial



          Then run aparcstats2table using
          aparc.pial instead of aparc (only
          because I called this new parcellation
          aparc.pial)



          To get the total surface area of each
          hemisphere I use:

          In the subject stats dir:


          mris_anatomical_stats -l
          ../label/lh.cortex.label -f
          lh.total_pial.stats -b SUBJ lh pial

          mris_anatomical_stats -l
          ../label/rh.cortex.label -f
          rh.total_pial.stats -b SUBJ rh pial

          Then run aparcstats2table using
          total_pial instead of aparc (again, only
          because I called this new parcellation
          total_pial. You may call it whatever
          you'd like)



          Just remeber to leave the specified dirs
          when creating the tables. If you dont't
          I think they will be created in the
          current dir.

          I use FS 5.0.

          Is this what you want?


          Best,
          Andreia



          Citando will brown
          <willbrown1987@gmail.com <mailto:willbrown1987@gmail.com>>:

                Hi all,
    I messed up this question recently so
    just want to clarify and try again. We
    want to know the cortical gray matter
    surface area of our subjects but are
    unclear about how to get this info.

    ?.aparc.stats reports:

    Measure Cortex, WhiteSurfArea, White
    Surface Total Area, XXXX, mm^2

    How about the gray matter?

    Thanks,
    Will





















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 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/

will brown

14 Sep 14 Sep

2:24 a.m.

Thanks Doug,

Just to double check I understand you correctly, where the output says "# Measure Cortex, WhiteSurfArea, White Surface Total Area" this is now the surface area of the pial surface even though it is labeled White?

Cheers, Will

On Sat, Sep 13, 2014 at 3:27 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

You can run something like

cd $SUBJECTS_DIR/subject

mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab subject lh pial

doug

On 09/11/2014 07:29 PM, will brown wrote:

...

We're using Freesurfer v5.3 on Centos 6.

Thanks, Will Brown

On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

sorry, this thread has gotten too deep. Can someone summarize the
question?


On Thu, 11 Sep 2014, _andreia_@sapo.pt <mailto:andreia_@sapo.pt>
wrote:


    Ok. Then, I'm not sure if everything is correct with the
    command lines since
    I use 5.0.

    Any thought on this Freesurfer team?

    Thanks,
    Andreia

    Citando will brown <willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>:

          Thanks again, for the record, I'm using freesurfer
    version 5.3.0
          on Centos 6.

          On 9/09/2014 11:00 PM, <_andreia_@sapo.pt
    <mailto:andreia_@sapo.pt>> wrote:

                Hi Will,

                Just to clarify, what version of FS are you using? I
                think it might not be 5.0 and I don't know if
                everything aplies if we are using different
                versions.


                1) Yes, it is only based on the pial surface (and
                these command lines are for the aparc, DK altas).
                The second set provides the surface area for each
                hemisphere without including, for example, the pial
                surface that you see in the hippocampus which is not
                accurate and one should not care about. In the end,
                the second set gives you the sum of the areas in
                aparc, thus, you can just make a sum of that
                parcellation if you want. I just realized that.

                2) No. In the new stats file, the value that you
                want is at the bottom:

                # ColHeaders StructName NumVert SurfArea GrayVol
                ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

                And when running aparcstats2table that's the value
                you should get in the table. I think that # Measure
                Cortex, WhiteSurfArea, White Surface Total Area may
                be including more stuff since it is bigger.


                If what you want is only the total hemisphere
                surface area you only need to run the second set of
                commands. If you want the area of each DK altas
                parcellation then run the first set and then simply
                add them to get total hemisphere surface area.


                Someone from Freesurfer staff will correct me if I'm
                wrong. (Please) I'm Ccing Doug since he was replying
                to your previous emails.

                Let's wait for their feedback.

                Andreia





                Citando will brown <willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>:

                      Thanks Andreia, this does appear to have
                      worked. Please forgive my ignorance but
                      I do just want to double check two
                      things;

    1) The first commands you have given provide the stats for
    the two hemispheres of the cerebral cortex only based on
    the pial surface, whereas the second set of commands
    provide the pial boundary stats for the whole brain rather
    than just cortex?

    2) The surface area value that I am looking for (grey
    matter surface area at the grey/pial boundary) is listed
    in the new stats table next to: # Measure Cortex,
    WhiteSurfArea, White Surface Total Area, ?

    Thanks again,
    Will

    On Tue, Sep 9, 2014 at 5:36 PM, will brown
    <willbrown1987@gmail.com <mailto:willbrown1987@gmail.com>> wrote:
          Thanks very much Andreia, yes this does look
          like what I want. I haven't had a chance to
          test it yet but it does indeed appear to
          answer my question. Thanks to those that have
          offered answers, to clarify, I did indeed mean
          the surface area of the pial surface rather
          than the white/grey boundary.
    Will


    On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt
    <mailto:andreia_@sapo.pt>>

    wrote:

          Hi Will,

          I use the following commands to get
          surface area from the pial surface:


          In the subject label dir:


          mris_anatomical_stats -mgz -cortex
          ../label/lh.cortex.label -f
          ../stats/lh.aparc.pial.stats -b -a
          ../label/lh.aparc.annot -c
          ../label/aparc.annot.ctab SUBJ lh pial

          mris_anatomical_stats -mgz -cortex
          ../label/rh.cortex.label -f
          ../stats/rh.aparc.pial.stats -b -a
          ../label/rh.aparc.annot -c
          ../label/aparc.annot.ctab SUBJ rh pial



          Then run aparcstats2table using
          aparc.pial instead of aparc (only
          because I called this new parcellation
          aparc.pial)



          To get the total surface area of each
          hemisphere I use:

          In the subject stats dir:


          mris_anatomical_stats -l
          ../label/lh.cortex.label -f
          lh.total_pial.stats -b SUBJ lh pial

          mris_anatomical_stats -l
          ../label/rh.cortex.label -f
          rh.total_pial.stats -b SUBJ rh pial

          Then run aparcstats2table using
          total_pial instead of aparc (again, only
          because I called this new parcellation
          total_pial. You may call it whatever
          you'd like)



          Just remeber to leave the specified dirs
          when creating the tables. If you dont't
          I think they will be created in the
          current dir.

          I use FS 5.0.

          Is this what you want?


          Best,
          Andreia



          Citando will brown
          <willbrown1987@gmail.com <mailto:willbrown1987@gmail.com>>:

                Hi all,
    I messed up this question recently so
    just want to clarify and try again. We
    want to know the cortical gray matter
    surface area of our subjects but are
    unclear about how to get this info.

    ?.aparc.stats reports:

    Measure Cortex, WhiteSurfArea, White
    Surface Total Area, XXXX, mm^2

    How about the gray matter?

    Thanks,
    Will





















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 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

15 Sep 15 Sep

10:53 a.m.

correct, unfortunately, the "White" label is hard coded into the program.

On 09/14/2014 02:24 AM, will brown wrote:

...

Thanks Doug,

Cheers, Will

On Sat, Sep 13, 2014 at 3:27 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

You can run something like

cd $SUBJECTS_DIR/subject

 mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
label/aparc.annot.ctab subject lh pial

The "Measure Cortex" fields in the output
stats/lh.aparc.pial.stats will be measures of the pial surface as
will the SurfArea, MeanCurv, GausCurv, FoldInd, and CurvInd fields
for each ROI (thickness and number of vertices will stay the same)

doug

On 09/11/2014 07:29 PM, will brown wrote:

    Sure. We'd like to know how to find the surface area of the
    cortical grey matter from the pial surface. So specifically,
    what is the surface area of the pial/grey matter boundary of
    the cortex for each hemisphere?

    We're using Freesurfer v5.3 on Centos 6.

    Thanks,
    Will Brown


    On Fri, Sep 12, 2014 at 9:11 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>>> wrote:

        sorry, this thread has gotten too deep. Can someone
    summarize the
        question?


        On Thu, 11 Sep 2014, _andreia_@sapo.pt
    <mailto:andreia_@sapo.pt> <mailto:andreia_@sapo.pt
    <mailto:andreia_@sapo.pt>>
        wrote:


            Ok. Then, I'm not sure if everything is correct with the
            command lines since
            I use 5.0.

            Any thought on this Freesurfer team?

            Thanks,
            Andreia

            Citando will brown <willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>
            <mailto:willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>>:

                  Thanks again, for the record, I'm using freesurfer
            version 5.3.0
                  on Centos 6.

                  On 9/09/2014 11:00 PM, <_andreia_@sapo.pt
    <mailto:andreia_@sapo.pt>
            <mailto:andreia_@sapo.pt <mailto:andreia_@sapo.pt>>>
    wrote:

                        Hi Will,

                        Just to clarify, what version of FS are
    you using? I
                        think it might not be 5.0 and I don't know if
                        everything aplies if we are using different
                        versions.


                        1) Yes, it is only based on the pial
    surface (and
                        these command lines are for the aparc, DK
    altas).
                        The second set provides the surface area
    for each
                        hemisphere without including, for example,
    the pial
                        surface that you see in the hippocampus
    which is not
                        accurate and one should not care about. In
    the end,
                        the second set gives you the sum of the
    areas in
                        aparc, thus, you can just make a sum of that
                        parcellation if you want. I just realized
    that.

                        2) No. In the new stats file, the value
    that you
                        want is at the bottom:

                        # ColHeaders StructName NumVert SurfArea
    GrayVol
                        ThickAvg ThickStd MeanCurv GausCurv
    FoldInd CurvInd

                        And when running aparcstats2table that's
    the value
                        you should get in the table. I think that
    # Measure
                        Cortex, WhiteSurfArea, White Surface Total
    Area may
                        be including more stuff since it is bigger.


                        If what you want is only the total hemisphere
                        surface area you only need to run the
    second set of
                        commands. If you want the area of each DK
    altas
                        parcellation then run the first set and
    then simply
                        add them to get total hemisphere surface area.


                        Someone from Freesurfer staff will correct
    me if I'm
                        wrong. (Please) I'm Ccing Doug since he
    was replying
                        to your previous emails.

                        Let's wait for their feedback.

                        Andreia





                        Citando will brown
    <willbrown1987@gmail.com <mailto:willbrown1987@gmail.com>
            <mailto:willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>>:

                              Thanks Andreia, this does appear to have
                              worked. Please forgive my ignorance but
                              I do just want to double check two
                              things;

            1) The first commands you have given provide the stats for
            the two hemispheres of the cerebral cortex only based on
            the pial surface, whereas the second set of commands
            provide the pial boundary stats for the whole brain rather
            than just cortex?

            2) The surface area value that I am looking for (grey
            matter surface area at the grey/pial boundary) is listed
            in the new stats table next to: # Measure Cortex,
            WhiteSurfArea, White Surface Total Area, ?

            Thanks again,
            Will

            On Tue, Sep 9, 2014 at 5:36 PM, will brown
            <willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>
    <mailto:willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>> wrote:
                  Thanks very much Andreia, yes this does look
                  like what I want. I haven't had a chance to
                  test it yet but it does indeed appear to
                  answer my question. Thanks to those that have
                  offered answers, to clarify, I did indeed mean
                  the surface area of the pial surface rather
                  than the white/grey boundary.
            Will


            On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt
    <mailto:andreia_@sapo.pt>
            <mailto:andreia_@sapo.pt <mailto:andreia_@sapo.pt>>>

            wrote:

                  Hi Will,

                  I use the following commands to get
                  surface area from the pial surface:


                  In the subject label dir:


                  mris_anatomical_stats -mgz -cortex
                  ../label/lh.cortex.label -f
                  ../stats/lh.aparc.pial.stats -b -a
                  ../label/lh.aparc.annot -c
                  ../label/aparc.annot.ctab SUBJ lh pial

                  mris_anatomical_stats -mgz -cortex
                  ../label/rh.cortex.label -f
                  ../stats/rh.aparc.pial.stats -b -a
                  ../label/rh.aparc.annot -c
                  ../label/aparc.annot.ctab SUBJ rh pial



                  Then run aparcstats2table using
                  aparc.pial instead of aparc (only
                  because I called this new parcellation
                  aparc.pial)



                  To get the total surface area of each
                  hemisphere I use:

                  In the subject stats dir:


                  mris_anatomical_stats -l
                  ../label/lh.cortex.label -f
                  lh.total_pial.stats -b SUBJ lh pial

                  mris_anatomical_stats -l
                  ../label/rh.cortex.label -f
                  rh.total_pial.stats -b SUBJ rh pial

                  Then run aparcstats2table using
                  total_pial instead of aparc (again, only
                  because I called this new parcellation
                  total_pial. You may call it whatever
                  you'd like)



                  Just remeber to leave the specified dirs
                  when creating the tables. If you dont't
                  I think they will be created in the
                  current dir.

                  I use FS 5.0.

                  Is this what you want?


                  Best,
                  Andreia



                  Citando will brown
                  <willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>
    <mailto:willbrown1987@gmail.com
    <mailto:willbrown1987@gmail.com>>>:

                        Hi all,
            I messed up this question recently so
            just want to clarify and try again. We
            want to know the cortical gray matter
            surface area of our subjects but are
            unclear about how to get this info.

            ?.aparc.stats reports:

            Measure Cortex, WhiteSurfArea, White
            Surface Total Area, XXXX, mm^2

            How about the gray matter?

            Thanks,
            Will





















        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 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

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

Douglas Greve

3 Sep 3 Sep

3:55 a.m.

That is the surface area of the cortical GM where it has its junction with the WM. Or do you want the surface area of the pial surface?

On 9/2/14 12:22 AM, will brown wrote:

...

Hi all,

I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.

?.aparc.stats reports:

Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2

How about the gray matter?

Thanks, Will

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

4329

Age (days ago)

4343

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

13 comments

6 participants

tags (0)

participants (6)

_andreia_＠sapo.pt
Bruce Fischl
Douglas Greve
Douglas N Greve
Krieger, Donald N.
will brown