I am encountering an odd effect when using the Freesurfer maps in Brainstorm. I have Individual activity for multiple subjects where the activity generally seems to look generally well spread across teh gyrus and sulcus in task relevant areas. However, when I map the individual subjects onto the freesurfer average anatomy, and average the activity it's primarily in the sulcus that the activity across subjects is prevalent. Most notably, it becomes heavily present in the Sylvian fissure.
I was looking through the mris_register function, and it seems the sulci are used as one of the primary alignment measures, and was wondering if this could be giving rise to this propensity of the group maps to appear predominantly in the sulcus. Looking through the settings I am not 100% clear on what all the settings do. So I was wondering if anyone had encountered this issue before. And what settings for the mris_register I should look at adjusting to try and correct the issue.
Thank you for your time and assistance.
Nicholas Heugel Biomedical Engineering Ph.D Candidate Marquette University
Hi Nicholas
I wouldn't think so. Look at the cortical parcellations and see if they are accurate. If they are it means that the cross-subject registration must be pretty good Bruce On Thu, 20 Oct 2016, Nicholas Heugel wrote:
I am encountering an odd effect when using the Freesurfer maps in Brainstorm. I have Individual activity for multiple subjects where the activity generally seems to look generally well spread across teh gyrus and sulcus in task relevant areas. However, when I map the individual subjects onto the freesurfer average anatomy, and average the activity it's primarily in the sulcus that the activity across subjects is prevalent. Most notably, it becomes heavily present in the Sylvian fissure.
I was looking through the mris_register function, and it seems the sulci are used as one of the primary alignment measures, and was wondering if this could be giving rise to this propensity of the group maps to appear predominantly in the sulcus. Looking through the settings I am not 100% clear on what all the settings do. So I was wondering if anyone had encountered this issue before. And what settings for the mris_register I should look at adjusting to try and correct the issue.
Thank you for your time and assistance.
Nicholas HeugelBiomedical Engineering Ph.D Candidate Marquette University
So just to be clear, If the individual cortical parcellations are accurate then what we observe isn't due to some quirk from the cross subject registration?
Nicholas Heugel Biomedical Engineering Ph.D Candidate Marquette University
On Thu, Oct 20, 2016 at 4:32 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Nicholas
I wouldn't think so. Look at the cortical parcellations and see if they are accurate. If they are it means that the cross-subject registration must be pretty good Bruce On Thu, 20 Oct 2016, Nicholas Heugel wrote:
I am encountering an odd effect when using the Freesurfer maps in
Brainstorm. I have Individual activity for multiple subjects where the activity generally seems to look generally well spread across teh gyrus and sulcus in task relevant areas. However, when I map the individual subjects onto the freesurfer average anatomy, and average the activity it's primarily in the sulcus that the activity across subjects is prevalent. Most notably, it becomes heavily present in the Sylvian fissure.
I was looking through the mris_register function, and it seems the sulci are used as one of the primary alignment measures, and was wondering if this could be giving rise to this propensity of the group maps to appear predominantly in the sulcus. Looking through the settings I am not 100% clear on what all the settings do. So I was wondering if anyone had encountered this issue before. And what settings for the mris_register I should look at adjusting to try and correct the issue.
Thank you for your time and assistance.
Nicholas HeugelBiomedical Engineering Ph.D Candidate Marquette University
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yes, I believe that is true
On Thu, 20 Oct 2016, Nicholas Heugel wrote:
So just to be clear, If the individual cortical parcellations are accurate then what we observe isn't due to some quirk from the cross subject registration?
Nicholas HeugelBiomedical Engineering Ph.D Candidate Marquette University
On Thu, Oct 20, 2016 at 4:32 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nicholas
I wouldn't think so. Look at the cortical parcellations and see if they are accurate. If they are it means that the cross-subject registration must be pretty good Bruce On Thu, 20 Oct 2016, Nicholas Heugel wrote: I am encountering an odd effect when using the Freesurfer maps in Brainstorm. I have Individual activity for multiple subjects where the activity generally seems to look generally well spread across teh gyrus and sulcus in task relevant areas. However, when I map the individual subjects onto the freesurfer average anatomy, and average the activity it's primarily in the sulcus that the activity across subjects is prevalent. Most notably, it becomes heavily present in the Sylvian fissure. I was looking through the mris_register function, and it seems the sulci are used as one of the primary alignment measures, and was wondering if this could be giving rise to this propensity of the group maps to appear predominantly in the sulcus. Looking through the settings I am not 100% clear on what all the settings do. So I was wondering if anyone had encountered this issue before. And what settings for the mris_register I should look at adjusting to try and correct the issue. Thank you for your time and assistance. Nicholas HeugelBiomedical Engineering Ph.D Candidate Marquette University _______________________________________________ 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.
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