Re: [Freesurfer] visualize subcortical areas in tksurfer?
Thanks, Bruce!! Daniel On Feb 23, 2015, at 8:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel I wouldn't advise this - you will miss most of the activation unless it happens to be right next to where the surface runs adjacent to the structure of interest. For subcortical structures you are better off showing the results in slices. cheers Bruce On Mon, 23 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks for the reply. My main question is how to best visualize subcortical activation in a figure. Sometimes we do see some subcortical activation (like the attached, which is a random search) (if the attachment does not work, please see the examplehere: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.frontiersin.org_files_Articles_18483_fnhum-2D06-2D00021-2DHTML_d=AwIDaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=FY2aLrzWyEp88KG_1MRXz7kOCWAb3NfLU7iRz6Ftg_4s=AsAyDkBwKH1FHSCReHATnZnHPXl7wm3478H1viSUbpce= image_m/fnhum-06-00021-g003.jpg). Is it okay to visualize such subcortical activation via tksurfer? If not, could you please recommend a method to visualize subcortical activation? Sincerely, Daniel On 2/20/15, 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . 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 ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli ancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZ GOKpGXPDgqUHYm=cue78znVQSK09ZAzgx1bpMEP_Q1FH_tPiP6u951nI6Is=FTUF8bxfkijut U0D90a6nXk4E6QXECVzI7RktBWSD04e= . 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compliancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=FY2aLrzWyEp88KG_1MRXz7kOCWAb3NfLU7iRz6Ftg_4s=ezWokB_ADNk3taLpmFv9QYfWH3gqVBCuqJA-NL9WIT8e= . If the e-mail was sent to you in error but does not
Re: [Freesurfer] visualize subcortical areas in tksurfer?
Hi Daniel I wouldn't advise this - you will miss most of the activation unless it happens to be right next to where the surface runs adjacent to the structure of interest. For subcortical structures you are better off showing the results in slices. cheers Bruce On Mon, 23 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks for the reply. My main question is how to best visualize subcortical activation in a figure. Sometimes we do see some subcortical activation (like the attached, which is a random search) (if the attachment does not work, please see the examplehere: http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/ image_m/fnhum-06-00021-g003.jpg). Is it okay to visualize such subcortical activation via tksurfer? If not, could you please recommend a method to visualize subcortical activation? Sincerely, Daniel On 2/20/15, 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . 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 ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli ancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZ GOKpGXPDgqUHYm=cue78znVQSK09ZAzgx1bpMEP_Q1FH_tPiP6u951nI6Is=FTUF8bxfkijut U0D90a6nXk4E6QXECVzI7RktBWSD04e= . 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] visualize subcortical areas in tksurfer?
Hi Bruce, Thanks for the reply. My main question is how to best visualize subcortical activation in a figure. Sometimes we do see some subcortical activation (like the attached, which is a random search) (if the attachment does not work, please see the example here: http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/image_m/fnhum-06-00021-g003.jpg). Is it okay to visualize such subcortical activation via tksurfer? If not, could you please recommend a method to visualize subcortical activation? Sincerely, Daniel On 2/20/15, 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . 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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compliancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=cue78znVQSK09ZAzgx1bpMEP_Q1FH_tPiP6u951nI6Is=FTUF8bxfkijutU0D90a6nXk4E6QXECVzI7RktBWSD04e= . 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] visualize subcortical areas in tksurfer?
Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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] visualize subcortical areas in tksurfer?
Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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] visualize subcortical areas in tksurfer?
Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . 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.
