Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not buggy in how it is calculated now. it is the area of the mid-point between the white and pial surfaces times the thickness at the vertex. The question that has been bandied about internally is whether this volume calculation should be corrected when it is mapped to the fsaverage surface during a group analysis (qdec does this mapping of the volume calcs of each subject to the fsaverage surface, when you select 'volume' as one of the measures). At some point we will visit this issue (and determine if it is an issue) but other stuff seems to take priority. Maybe someone on the list can chime in.
Nick
On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is there now actually a "mid" surface available in between the white and pial surfaces? (i.e., akin to Caret)? Or by "area of the mid-point" are you just referring to the average at each vertex of the ?h.area and ? h.area.pial "curv" files?
thanks, -Mike H.
On Tue, 2009-02-17 at 13:17 -0500, Nick Schmansky wrote:
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not buggy in how it is calculated now. it is the area of the mid-point between the white and pial surfaces times the thickness at the vertex. The question that has been bandied about internally is whether this volume calculation should be corrected when it is mapped to the fsaverage surface during a group analysis (qdec does this mapping of the volume calcs of each subject to the fsaverage surface, when you select 'volume' as one of the measures). At some point we will visit this issue (and determine if it is an issue) but other stuff seems to take priority. Maybe someone on the list can chime in.
Nick
On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mike,
we don't generate the mid surface by default, but there is code around to do so if you want to. You can use:
mris_expand -thickness lh.white 0.5 lh.midgray
to generate it I think. cheers, Bruce
On Tue, 17 Feb 2009, Michael Harms wrote:
Is there now actually a "mid" surface available in between the white and pial surfaces? (i.e., akin to Caret)? Or by "area of the mid-point" are you just referring to the average at each vertex of the ?h.area and ? h.area.pial "curv" files?
thanks, -Mike H.
On Tue, 2009-02-17 at 13:17 -0500, Nick Schmansky wrote:
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not buggy in how it is calculated now. it is the area of the mid-point between the white and pial surfaces times the thickness at the vertex. The question that has been bandied about internally is whether this volume calculation should be corrected when it is mapped to the fsaverage surface during a group analysis (qdec does this mapping of the volume calcs of each subject to the fsaverage surface, when you select 'volume' as one of the measures). At some point we will visit this issue (and determine if it is an issue) but other stuff seems to take priority. Maybe someone on the list can chime in.
Nick
On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Mike,
The 'area of the mid-point' calculation is made by averaging the ?h.area and ?h.area_pial data files (the ?h.area file contains the area of the white surface). This is done in recon-all using mris_calc, and outputs ?h.area_mid.
Nick
On Tue, 2009-02-17 at 12:41 -0600, Michael Harms wrote:
Is there now actually a "mid" surface available in between the white and pial surfaces? (i.e., akin to Caret)? Or by "area of the mid-point" are you just referring to the average at each vertex of the ?h.area and ? h.area.pial "curv" files?
thanks, -Mike H.
On Tue, 2009-02-17 at 13:17 -0500, Nick Schmansky wrote:
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not buggy in how it is calculated now. it is the area of the mid-point between the white and pial surfaces times the thickness at the vertex. The question that has been bandied about internally is whether this volume calculation should be corrected when it is mapped to the fsaverage surface during a group analysis (qdec does this mapping of the volume calcs of each subject to the fsaverage surface, when you select 'volume' as one of the measures). At some point we will visit this issue (and determine if it is an issue) but other stuff seems to take priority. Maybe someone on the list can chime in.
Nick
On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It seems like the issue of whether or not to correct the volume when mapping to fsaverage is akin to the choice of "modulated" vs. "non- modulated" VBM, as it's called...
-MH
On Tue, 2009-02-17 at 13:17 -0500, Nick Schmansky wrote:
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not buggy in how it is calculated now. it is the area of the mid-point between the white and pial surfaces times the thickness at the vertex. The question that has been bandied about internally is whether this volume calculation should be corrected when it is mapped to the fsaverage surface during a group analysis (qdec does this mapping of the volume calcs of each subject to the fsaverage surface, when you select 'volume' as one of the measures). At some point we will visit this issue (and determine if it is an issue) but other stuff seems to take priority. Maybe someone on the list can chime in.
Nick
On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, it's the same, and modulated (or Jacobian corrected) is definitely the right thing to do IMO On Tue, 17 Feb 2009, Michael Harms wrote:
It seems like the issue of whether or not to correct the volume when mapping to fsaverage is akin to the choice of "modulated" vs. "non- modulated" VBM, as it's called...
-MH
On Tue, 2009-02-17 at 13:17 -0500, Nick Schmansky wrote:
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not buggy in how it is calculated now. it is the area of the mid-point between the white and pial surfaces times the thickness at the vertex. The question that has been bandied about internally is whether this volume calculation should be corrected when it is mapped to the fsaverage surface during a group analysis (qdec does this mapping of the volume calcs of each subject to the fsaverage surface, when you select 'volume' as one of the measures). At some point we will visit this issue (and determine if it is an issue) but other stuff seems to take priority. Maybe someone on the list can chime in.
Nick
On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think the area probably should be corrected to preserve the native area of the subject, but as you say we haven't gotten to the correction yet. On Tue, 17 Feb 2009, Nick Schmansky wrote:
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not buggy in how it is calculated now. it is the area of the mid-point between the white and pial surfaces times the thickness at the vertex. The question that has been bandied about internally is whether this volume calculation should be corrected when it is mapped to the fsaverage surface during a group analysis (qdec does this mapping of the volume calcs of each subject to the fsaverage surface, when you select 'volume' as one of the measures). At some point we will visit this issue (and determine if it is an issue) but other stuff seems to take priority. Maybe someone on the list can chime in.
Nick
On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct?
Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed?
I greatly appreciate any help in this matter.
Thank you, Devdutta _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Devdutta W -
Michael Harms -
Nick Schmansky