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
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
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
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
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
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 -flh.TOTAL_PIAL.stats -b SUBJ lh pial_
_mris_anatomical_stats -l ../label/rh.cortex.label -frh.TOTAL_PIAL.stats -b SUBJ rh pial_
_Then run aparcstats2table using TOTAL_PIAL instead ofaparc (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_ _ _ _ _
_ _
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*
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 brownwillbrown1987@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 insteadof 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__ __ __ __ __
_ _ __ __
_ _
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
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.
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> 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.
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
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> 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/
correct, unfortunately, the "White" label is hard coded into the program.
On 09/14/2014 02:24 AM, will brown wrote:
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 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/
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
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