Re: [Freesurfer] Editing masks
Hello Bruce, Yes, I am using the surfaces for this. I am trying to find cortical thickness differences between populations. I do not think that the mask covers the entire hippocampal area, just leaving out the corpus callosum. How would I include these areas into the mask? Thank you, Joshua On Tue, Jun 11, 2013 at 8:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Joshua are you using the surfaces for this? If so, you shouldn't as they are undefined in those regions (since they have internal laminar structure that is different than what we expect). What are you trying to achieve? cheers Bruce On Tue, 11 Jun 2013, Joshua deSouza wrote: Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua 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/**compliancelinehttp://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.
Re: [Freesurfer] Editing masks
Hi Joshua The thickness isn't well defined in the hippocampus, so you don't want to use it there. Use volumes of the subfields instead Cheers Bruce On Jun 12, 2013, at 10:35 PM, Joshua deSouza desouzajoshu...@gmail.com wrote: Hello Bruce, Yes, I am using the surfaces for this. I am trying to find cortical thickness differences between populations. I do not think that the mask covers the entire hippocampal area, just leaving out the corpus callosum. How would I include these areas into the mask? Thank you, Joshua On Tue, Jun 11, 2013 at 8:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Joshua are you using the surfaces for this? If so, you shouldn't as they are undefined in those regions (since they have internal laminar structure that is different than what we expect). What are you trying to achieve? cheers Bruce On Tue, 11 Jun 2013, Joshua deSouza wrote: Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua 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] Editing masks
Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua ___ 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.
Re: [Freesurfer] Editing masks
Hi Joshua are you using the surfaces for this? If so, you shouldn't as they are undefined in those regions (since they have internal laminar structure that is different than what we expect). What are you trying to achieve? cheers Bruce On Tue, 11 Jun 2013, Joshua deSouza wrote: Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua ___ 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] editing masks
Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I was wondering though how I might go about editing the mask? I see that there are random voxels that have been left out and I would like to fill those in. Thanks Dan -- Daniel Horim Choi Northwestern University Class of 2009 [EMAIL PROTECTED] or [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] editing masks
Sorry, I don't understand. Where did you get the mask? Or are you trying to create it from scratch? On Tue, 5 Aug 2008, Daniel H Choi wrote: Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I was wondering though how I might go about editing the mask? I see that there are random voxels that have been left out and I would like to fill those in. Thanks Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
