Hello FreeSurfer experts,
I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
Hello Bruce,
Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
Hi Paul
if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing
cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Bruce,
Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing
cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Paul
I guess you could use CVS for this.
cheers Bruce On Sat, 14 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing
cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
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
Hello Bruce,
Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2 --step3 --outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?
My next goals are to: 1) sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using mri_vol2vol -reg . -which of the outputs from mri_cvs_register should i use to achieve? final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz
2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol. - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm.
3) Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on them. - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage?
Thank you very much
Best, Paul
On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Paul
I guess you could use CVS for this.
cheers Bruce
On Sat, 14 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing
cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts,
I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
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
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.
---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Sat, Oct 14, 2017 at 3:32 PM Subject: Re: [Freesurfer] cortical/subcortical volume based analysis To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Bruce,
Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2 --step3 --outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?
My next goals are to: 1) sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using mri_vol2vol -reg . -which of the outputs from mri_cvs_register should i use to achieve? final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz
2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol. - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm.
3) Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on them. - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage?
Thank you very much
Best, Paul
On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Paul
I guess you could use CVS for this.
cheers Bruce
On Sat, 14 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing
cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts,
I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
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
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 Paul
I was waiting for Lilla to respond :) Bruce On Wed, 18 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
I wasn't sure if you answered my previous message hence, I'm sending it again. Thank you.
Best, Paul
---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Sat, Oct 14, 2017 at 3:32 PM Subject: Re: [Freesurfer] cortical/subcortical volume based analysis To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2 --step3 --outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?
My next goals are to:
- sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using
mri_vol2vol -reg . -which of the outputs from mri_cvs_register should i use to achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz 2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol. - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm.
- Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on
them. - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage?
Thank you very much
Best, Paul
On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Paul
I guess you could use CVS for this. cheers Bruce On Sat, 14 Oct 2017, miracle ozzoude wrote: Hello Bruce, Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm? Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis Hi Paul if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello Bruce, Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation? Best, Miracle Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis Hi Paul we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much. Best, Paul _______________________________________________ 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
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.
Hello Bruce,
Thank you very much for the update.
Best Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Wednesday, October 18, 2017 8:20 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Fwd: cortical/subcortical volume based analysis
Hi Paul
I was waiting for Lilla to respond :) Bruce On Wed, 18 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
I wasn't sure if you answered my previous message hence, I'm sending it again. Thank you.
Best, Paul
---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Sat, Oct 14, 2017 at 3:32 PM Subject: Re: [Freesurfer] cortical/subcortical volume based analysis To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2 --step3 --outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?
My next goals are to:
- sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using
mri_vol2vol -reg . -which of the outputs from mri_cvs_register should i use to achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz 2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol. - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm.
- Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on
them. - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage?
Thank you very much
Best, Paul
On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Paul
I guess you could use CVS for this.
cheers Bruce On Sat, 14 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing
cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
we typically do this type of analysis by looking at scatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface based group analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul
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Hello Bruce,
I am still waiting on your response or Lilla's. Thank you.
Best, Paul
On Wed, Oct 18, 2017 at 8:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Paul
I was waiting for Lilla to respond :) Bruce
On Wed, 18 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
I wasn't sure if you answered my previous message hence, I'm sending it again. Thank you.
Best, Paul
---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Sat, Oct 14, 2017 at 3:32 PM Subject: Re: [Freesurfer] cortical/subcortical volume based analysis To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2 --step3 --outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?
My next goals are to:
- sample the volumes created using mri_cvs_register to the
cvs_avg35_inMNI152 template using mri_vol2vol -reg . -which of the outputs from mri_cvs_register should i use to achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz 2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol. - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm.
- Lastly, use mri_concat to combine the smoothened maps in order to
perform group level analysis on them. - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage?
Thank you very much
Best, Paul
On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Paul
I guess you could use CVS for this. cheers Bruce On Sat, 14 Oct 2017, miracle ozzoude wrote: Hello Bruce, Thank you very much. Can I still general cortical andsubcortical maps with the Spherical warp of r/lh.white surface? If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?
Best, Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Saturday, October 14, 2017 11:27 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volume basedanalysis
Hi Paul if you use a property (like gm) to drive intersubjectregistration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the warp field would the effect move somewhere else?). If the warp is not perfect then some of the effect is in your warp and some in the residual anatomical differences. There are lots of caveats like this you have to worry about. It's the reason we drive our spherical warp with the ?h.white surface. It is invariant to gm atrophy and so can be used to assess it without worrying about this kind of thing
cheers Bruce On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello Bruce, Thank you for the response. I meant the latter ( makingmaps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation?
Best, Miracle Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, October 13, 2017 6:53 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] cortical/subcortical volumebased analysis
Hi Paul we typically do this type of analysis by looking atscatter plots of structure volumes (e.g. hippocampus). Alternatively, you can make maps, but that opens up all the problems/difficulties of interpretation of VBM. Which did you mean? cheers Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote: Hello FreeSurfer experts, I want to perform a whole brain volume based group analysis for cortical and subcortical regions. That's something very similar to surface basedgroup analysis for cortical thickness however, for volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can someone direct me how to go about doing it? My goal is to perform a group comparison between control and PD patients based on volume. Thank you very much.
Best, Paul _______________________________________________ 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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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.
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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.
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miracle ozzoude