Hi FS experts,
I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue?
Thank you for your time, Panos
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain.
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS experts,
I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue?
Thank you for your time, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient).
Thank you again for your time! Panos
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain.
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS experts,
I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue?
Thank you for your time, Panos _______________________________________________ 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 see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate - that wouldn't be a problem. You just don't want to measure it that way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient).
Thank you again for your time! Panos
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain.
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS experts,
I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue?
Thank you for your time, Panos _______________________________________________ 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
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Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos
I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient).
Thank you again for your time! Panos
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain.
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS experts,
I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue?
Thank you for your time, Panos _______________________________________________ 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
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Hi Panos
I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos
I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient).
Thank you again for your time! Panos
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain.
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS experts,
I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue?
Thank you for your time, Panos _______________________________________________ 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
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Bruce,
I see, that's really helpful, thank you!
Best, Panos
Hi Panos
I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos
I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that
way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient).
Thank you again for your time! Panos
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain.
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS experts,
I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue?
Thank you for your time, Panos _______________________________________________ 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
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Hi Bruce,
Sorry, I had a last follow up question. I just realized that the resulting bins will be in the fsaverage space, and hence I wouldn't be able to use mris_anatomical_stats to calculate the average thickness of the bins, since the fsaverage "subject" does not have a wm.mgz file. Did you have another way in mind to calculate the thickness of each bin, or do you believe that mris_anatomical stats should do the trick with a specific flag?
Thanks a ton, Panos
Hi Bruce,
I see, that's really helpful, thank you!
Best, Panos
Hi Panos
I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos
I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that
way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient).
Thank you again for your time! Panos
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain.
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
> Hi FS experts, > > I was wondering whether it would be possible to measure the average > cortical thickness at a specific slice (either axial, coronal, or > sagittal). I read in Bruce's paper: "Measuring the thickness of the > human > cerebral cortex from magnetic resonance images" that "Measuring the > thickness from the coronal slice at the point indicated by the > green > cross > would result in an estimate in excess of 1 cm." Is that always the > case, > or has there been a way to bypass that issue? > > Thank you for your time, > Panos > _______________________________________________ > 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
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Hi Panos
no, mris_anatomical_stats won't do it. I would map the average thickness to fsaverage coords, then load that into matlab and go from there using the [xyz] coords of fsaverage for the binning, which is pretty much MNI305
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Sorry, I had a last follow up question. I just realized that the resulting bins will be in the fsaverage space, and hence I wouldn't be able to use mris_anatomical_stats to calculate the average thickness of the bins, since the fsaverage "subject" does not have a wm.mgz file. Did you have another way in mind to calculate the thickness of each bin, or do you believe that mris_anatomical stats should do the trick with a specific flag?
Thanks a ton, Panos
Hi Bruce,
I see, that's really helpful, thank you!
Best, Panos
Hi Panos
I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos
I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that
way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient).
Thank you again for your time! Panos
> Hi Panos > > it would certainly be possible to make that measurement, but it > wouldn't > tell you anything biologically interesting. Why would you want to do > such > a > thing? It will reflect the (arbitrary) image slice orientation and > not > the > brain. > > cheers > Bruce > > > On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote: > >> Hi FS experts, >> >> I was wondering whether it would be possible to measure the average >> cortical thickness at a specific slice (either axial, coronal, or >> sagittal). I read in Bruce's paper: "Measuring the thickness of the >> human >> cerebral cortex from magnetic resonance images" that "Measuring the >> thickness from the coronal slice at the point indicated by the >> green >> cross >> would result in an estimate in excess of 1 cm." Is that always the >> case, >> or has there been a way to bypass that issue? >> >> Thank you for your time, >> Panos >> _______________________________________________ >> 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 > > >
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Hi Bruce,
I was having issues with the part after that, that is how to calculate the average thickness of those bins, after I create them. Thanks again Best, Panos
Hi Panos
no, mris_anatomical_stats won't do it. I would map the average thickness to fsaverage coords, then load that into matlab and go from there using the [xyz] coords of fsaverage for the binning, which is pretty much MNI305
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Sorry, I had a last follow up question. I just realized that the resulting bins will be in the fsaverage space, and hence I wouldn't be able to use mris_anatomical_stats to calculate the average thickness of the bins, since the fsaverage "subject" does not have a wm.mgz file. Did you have another way in mind to calculate the thickness of each bin, or do you believe that mris_anatomical stats should do the trick with a specific flag?
Thanks a ton, Panos
Hi Bruce,
I see, that's really helpful, thank you!
Best, Panos
Hi Panos
I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos
I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that
way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
> Hi Bruce, > > Thank you for your reply. I was interested in looking how the > thickness > changes from the posterior to the anterior side of the brain and > vice > versa (the thickness gradient). > > Thank you again for your time! > Panos > > >> Hi Panos >> >> it would certainly be possible to make that measurement, but it >> wouldn't >> tell you anything biologically interesting. Why would you want to >> do >> such >> a >> thing? It will reflect the (arbitrary) image slice orientation and >> not >> the >> brain. >> >> cheers >> Bruce >> >> >> On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote: >> >>> Hi FS experts, >>> >>> I was wondering whether it would be possible to measure the >>> average >>> cortical thickness at a specific slice (either axial, coronal, or >>> sagittal). I read in Bruce's paper: "Measuring the thickness of >>> the >>> human >>> cerebral cortex from magnetic resonance images" that "Measuring >>> the >>> thickness from the coronal slice at the point indicated by the >>> green >>> cross >>> would result in an estimate in excess of 1 cm." Is that always >>> the >>> case, >>> or has there been a way to bypass that issue? >>> >>> Thank you for your time, >>> Panos >>> _______________________________________________ >>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Bruce,
Thanks again for your help so far. I had a few follow up questions:
1) As far as mapping the average thickness to fsaverage coords, when I was constructing the average thickness map I used mris_preproc with --target fsaverage (and then mri_concat), so it's already in fsaverage coordinates right? Or do I need to apply mri_surf2surf?
2) I used read_curv to load it into matlab which gives a <n*1> matrix where I'm assuming that n is the number of total vertices of the cortex, right?
3) Concerning the binning in matlab, I know how to do it in the order of increasing vertex number, but I had trouble incorporating the [xyz] fsaverage coordinates. Is there a way to rearrange the matrix (that is the result of read_curv) into another matrix where the thickness values are sorted based on the fsaverage coordinates?
Best, Panos
Hi Panos
no, mris_anatomical_stats won't do it. I would map the average thickness to fsaverage coords, then load that into matlab and go from there using the [xyz] coords of fsaverage for the binning, which is pretty much MNI305
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Sorry, I had a last follow up question. I just realized that the resulting bins will be in the fsaverage space, and hence I wouldn't be able to use mris_anatomical_stats to calculate the average thickness of the bins, since the fsaverage "subject" does not have a wm.mgz file. Did you have another way in mind to calculate the thickness of each bin, or do you believe that mris_anatomical stats should do the trick with a specific flag?
Thanks a ton, Panos
Hi Bruce,
I see, that's really helpful, thank you!
Best, Panos
Hi Panos
I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate
cheers Bruce On Tue, 13 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P coordinate" do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P->A, or is there another way to find the average thickness of each slice and then see how that average changes from P->A? Thanks again for your time, Panos
I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that
way
cheers Bruce
On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote:
> Hi Bruce, > > Thank you for your reply. I was interested in looking how the > thickness > changes from the posterior to the anterior side of the brain and > vice > versa (the thickness gradient). > > Thank you again for your time! > Panos > > >> Hi Panos >> >> it would certainly be possible to make that measurement, but it >> wouldn't >> tell you anything biologically interesting. Why would you want to >> do >> such >> a >> thing? It will reflect the (arbitrary) image slice orientation and >> not >> the >> brain. >> >> cheers >> Bruce >> >> >> On Mon, 12 May 2014, pfotiad@nmr.mgh.harvard.edu wrote: >> >>> Hi FS experts, >>> >>> I was wondering whether it would be possible to measure the >>> average >>> cortical thickness at a specific slice (either axial, coronal, or >>> sagittal). I read in Bruce's paper: "Measuring the thickness of >>> the >>> human >>> cerebral cortex from magnetic resonance images" that "Measuring >>> the >>> thickness from the coronal slice at the point indicated by the >>> green >>> cross >>> would result in an estimate in excess of 1 cm." Is that always >>> the >>> case, >>> or has there been a way to bypass that issue? >>> >>> Thank you for your time, >>> Panos >>> _______________________________________________ >>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
pfotiad＠nmr.mgh.harvard.edu