Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume).
Thank you very much, Florence Campana
How did you get your ICA analysis into MNI305 (or MNI152) space? You're ICA intergroup comparisons will only be as good as that space -- how you get it onto the surface from there is not so important. You can run recon-all on the MNI152, sample the ICA maps onto the surface, then use the surface-based registration to map it to fsaverage.
On 10/9/17 7:20 PM, Florence Campana wrote:
Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume).
Thank you very much, Florence Campana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I¹d note that you can run the group ICA on surface data in surface space pretty easily using melodic, which would avoid the issue that Doug mentions.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 7:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Transformation between spaces
How did you get your ICA analysis into MNI305 (or MNI152) space? You're ICA intergroup comparisons will only be as good as that space -- how you get it onto the surface from there is not so important. You can run recon-all on the MNI152, sample the ICA maps onto the surface, then use the surface-based registration to map it to fsaverage.
On 10/9/17 7:20 PM, Florence Campana wrote:
Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume).
Thank you very much,
Florence Campana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinf o/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 Matt,
Thank you for your quick input ; I did not try yet to use melodic, it seems indeed to be the most straightforward solution, I will try it, thank you again!
Florence
Le lundi 9 octobre 2017, Matt Glasser <matt@ma-tea.com javascript:_e(%7B%7D,'cvml','matt@ma-tea.com');> a écrit :
I’d note that you can run the group ICA on surface data in surface space pretty easily using melodic, which would avoid the issue that Doug mentions.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 7:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Transformation between spaces
How did you get your ICA analysis into MNI305 (or MNI152) space? You're ICA intergroup comparisons will only be as good as that space -- how you get it onto the surface from there is not so important. You can run recon-all on the MNI152, sample the ICA maps onto the surface, then use the surface-based registration to map it to fsaverage.
On 10/9/17 7:20 PM, Florence Campana wrote:
Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume).
Thank you very much, Florence Campana
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e du/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/compli anceline . 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 latest version of melodic is compatible with CIFTI data (e.g. From the HCP).
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Florence Campana campana.florence@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 9:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Transformation between spaces
Hi Matt,
Thank you for your quick input ; I did not try yet to use melodic, it seems indeed to be the most straightforward solution, I will try it, thank you again!
Florence
Le lundi 9 octobre 2017, Matt Glasser <matt@ma-tea.com javascript:_e(%7B%7D,'cvml','matt@ma-tea.com'); > a écrit :
I¹d note that you can run the group ICA on surface data in surface space pretty easily using melodic, which would avoid the issue that Doug mentions.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 7:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Transformation between spaces
How did you get your ICA analysis into MNI305 (or MNI152) space? You're ICA intergroup comparisons will only be as good as that space -- how you get it onto the surface from there is not so important. You can run recon-all on the MNI152, sample the ICA maps onto the surface, then use the surface-based registration to map it to fsaverage.
On 10/9/17 7:20 PM, Florence Campana wrote:
Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume).
Thank you very much,
Florence Campana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listin fo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinf o/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.
_______________________________________________ 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 Matt,
I follow-up on your suggestion of running MELODIC in surface. I am unsure about the registration files that I should use (I guess that they should be surface files?), notably for the Main Structural Images and the Standard Space. I am sorry if this sounds like a naive question.
Thank you very much,
Florence
2017-10-09 22:28 GMT-04:00 Matt Glasser matt@ma-tea.com:
The latest version of melodic is compatible with CIFTI data (e.g. From the HCP).
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Florence Campana campana.florence@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 9:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Transformation between spaces
Hi Matt,
Thank you for your quick input ; I did not try yet to use melodic, it seems indeed to be the most straightforward solution, I will try it, thank you again!
Florence
Le lundi 9 octobre 2017, Matt Glasser matt@ma-tea.com a écrit :
I’d note that you can run the group ICA on surface data in surface space pretty easily using melodic, which would avoid the issue that Doug mentions.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 7:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Transformation between spaces
How did you get your ICA analysis into MNI305 (or MNI152) space? You're ICA intergroup comparisons will only be as good as that space -- how you get it onto the surface from there is not so important. You can run recon-all on the MNI152, sample the ICA maps onto the surface, then use the surface-based registration to map it to fsaverage.
On 10/9/17 7:20 PM, Florence Campana wrote:
Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume).
Thank you very much, Florence Campana
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.e du/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.
_______________________________________________ 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.
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.
You would be running melodic from the command line. If you have further questions on CIFTI, the better place to ask would be the HCP-Users mailing list:
https://www.humanconnectome.org/contact-us
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Florence Campana campana.florence@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, October 10, 2017 at 12:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Transformation between spaces
Hi Matt,
I follow-up on your suggestion of running MELODIC in surface. I am unsure about the registration files that I should use (I guess that they should be surface files?), notably for the Main Structural Images and the Standard Space. I am sorry if this sounds like a naive question.
Thank you very much,
Florence
2017-10-09 22:28 GMT-04:00 Matt Glasser matt@ma-tea.com:
The latest version of melodic is compatible with CIFTI data (e.g. From the HCP).
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Florence Campana campana.florence@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 9:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Transformation between spaces
Hi Matt,
Thank you for your quick input ; I did not try yet to use melodic, it seems indeed to be the most straightforward solution, I will try it, thank you again!
Florence
Le lundi 9 octobre 2017, Matt Glasser matt@ma-tea.com a écrit :
I¹d note that you can run the group ICA on surface data in surface space pretty easily using melodic, which would avoid the issue that Doug mentions.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, October 9, 2017 at 7:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Transformation between spaces
How did you get your ICA analysis into MNI305 (or MNI152) space? You're ICA intergroup comparisons will only be as good as that space -- how you get it onto the surface from there is not so important. You can run recon-all on the MNI152, sample the ICA maps onto the surface, then use the surface-based registration to map it to fsaverage.
On 10/9/17 7:20 PM, Florence Campana wrote:
Dear freesurfer experts,
I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume).
Thank you very much,
Florence Campana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi nfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listin fo/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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinf o/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.
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.
_______________________________________________ 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.
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Florence Campana -
Matt Glasser