Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab. I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction. Thanks!
Best,Yue
Hi Yue
if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in.
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab.
I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction.
Thanks!
Best, Yue
Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in those regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot!
Best,Yue> Date: Fri, 1 Nov 2013 08:45:35 -0400
From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in one anatomical region?
Hi Yue
if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in.
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab.
I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction.
Thanks!
Best, Yue
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.
Hi Yue
tksurfer will only display cortical histograms. For subcortical regions you are probably best off using something like matlab (which would be pretty trivial)
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in those regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot!
Best, Yue
Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in one
anatomical region?
Hi Yue
if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in.
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate
surfaces
and labels in freesurfer. Then I would like to do statistical analysis
in
the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can
display
these regions in different color in freeview based on the look-up table
but
I don't know how to use them to generate histograms in freesurfer or
create
binary masks then I can do the analysis with these masks in matlab.
I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional
masks
for a group study. I am new to freesurfer and I really appreciate if
someone
can point out a direction.
Thanks!
Best, Yue
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
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.
Hi Bruce, Thanks for responding so quickly. Sorry I probably don't describe my question clearly and my examples are bad. This is really new to me. So please correct me if I say something wrong. Let me explain again. Hopefully it will make some sense. What I want to do is first to segment out different cortical and subcorical regions(like frontal cortex, occipital cortex, posterior cingulate cortex, putamen etc.) and then generate histograms from these regions separately. The surfaces give me the histograms that only include the intensities on the edges of the regions, right? I am wondering if I can generate histograms from the area of one cortical region not just the boundaries. Thanks!
Best,Yue
Date: Fri, 1 Nov 2013 11:12:46 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to generate histograms of intensities in one anatomical region?
Hi Yue
tksurfer will only display cortical histograms. For subcortical regions you are probably best off using something like matlab (which would be pretty trivial)
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in those regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot!
Best, Yue
Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in one
anatomical region?
Hi Yue
if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in.
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate
surfaces
and labels in freesurfer. Then I would like to do statistical analysis
in
the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can
display
these regions in different color in freeview based on the look-up table
but
I don't know how to use them to generate histograms in freesurfer or
create
binary masks then I can do the analysis with these masks in matlab.
I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional
masks
for a group study. I am new to freesurfer and I really appreciate if
someone
can point out a direction.
Thanks!
Best, Yue
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
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.
the surfaces can be used to sample in many different ways using options to mri_vol2surf. For example you could average over the ribbon then display the histogram of that. For subcortical structures the surfaces don't make sense, so you are better off just doing it in matlab cheers Bruce
On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce, Thanks for responding so quickly.
Sorry I probably don't describe my question clearly and my examples are bad. This is really new to me. So please correct me if I say something wrong. Let me explain again. Hopefully it will make some sense.
What I want to do is first to segment out different cortical and subcorical regions(like frontal cortex, occipital cortex, posterior cingulate cortex, putamen etc.) and then generate histograms from these regions separately. The surfaces give me the histograms that only include the intensities on the edges of the regions, right? I am wondering if I can generate histograms from the area of one cortical region not just the boundaries. Thanks!
Best, Yue
Date: Fri, 1 Nov 2013 11:12:46 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to generate histograms of intensities in one
anatomical region?
Hi Yue
tksurfer will only display cortical histograms. For subcortical regions you are probably best off using something like matlab (which would be pretty trivial)
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in
those
regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot!
Best, Yue
Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in
one
anatomical region?
Hi Yue
if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can
also
use mask_label to remove values outside of an ROI if that is what you
are
interested in.
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate
surfaces
and labels in freesurfer. Then I would like to do statistical
analysis
in
the regions I am interested in. For example, I would like to
generate a
histogram of intensities in frontal cortex or in occipital. I can
display
these regions in different color in freeview based on the look-up
table
but
I don't know how to use them to generate histograms in freesurfer or
create
binary masks then I can do the analysis with these masks in matlab.
I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create
regional
masks
for a group study. I am new to freesurfer and I really appreciate if
someone
can point out a direction.
Thanks!
Best, Yue
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
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.
Got you. I will check out ribbon and read more about mri_vol2surf. Thanks for your help! Yue
Date: Fri, 1 Nov 2013 12:16:48 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to generate histograms of intensities in one anatomical region?
the surfaces can be used to sample in many different ways using options to mri_vol2surf. For example you could average over the ribbon then display the histogram of that. For subcortical structures the surfaces don't make sense, so you are better off just doing it in matlab cheers Bruce
On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce, Thanks for responding so quickly.
Sorry I probably don't describe my question clearly and my examples are bad. This is really new to me. So please correct me if I say something wrong. Let me explain again. Hopefully it will make some sense.
What I want to do is first to segment out different cortical and subcorical regions(like frontal cortex, occipital cortex, posterior cingulate cortex, putamen etc.) and then generate histograms from these regions separately. The surfaces give me the histograms that only include the intensities on the edges of the regions, right? I am wondering if I can generate histograms from the area of one cortical region not just the boundaries. Thanks!
Best, Yue
Date: Fri, 1 Nov 2013 11:12:46 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to generate histograms of intensities in one
anatomical region?
Hi Yue
tksurfer will only display cortical histograms. For subcortical regions you are probably best off using something like matlab (which would be pretty trivial)
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in
those
regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot!
Best, Yue
Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fischl@nmr.mgh.harvard.edu To: moonblue412@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in
one
anatomical region?
Hi Yue
if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can
also
use mask_label to remove values outside of an ROI if that is what you
are
interested in.
cheers Bruce On Fri, 1 Nov 2013, ?? wrote:
Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate
surfaces
and labels in freesurfer. Then I would like to do statistical
analysis
in
the regions I am interested in. For example, I would like to
generate a
histogram of intensities in frontal cortex or in occipital. I can
display
these regions in different color in freeview based on the look-up
table
but
I don't know how to use them to generate histograms in freesurfer or
create
binary masks then I can do the analysis with these masks in matlab.
I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create
regional
masks
for a group study. I am new to freesurfer and I really appreciate if
someone
can point out a direction.
Thanks!
Best, Yue
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in
error
but does not contain patient information, please contact the sender
and
properly
dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
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