Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi Sabin, I have not been able to definitively track down the source of the negative area, but I have verified a couple of things. There is only negative area in a couple of vertices and they are in the medial wall. Our current development version does not result in negative area when I run it on your data, so what ever is happening has been fixed. In general, the area from the current development version is very close to that of what you have, so I think the negative area can be ignored. doug On 04/17/2014 12:47 PM, sabin khadka wrote: Hi all, I ran mri_surf2surf and then mris_convert to get vertexwise thickness and surface area values in ascii files. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:30 AM, sabin khadka sabink...@yahoo.com wrote: Ahh. Great. Thanks you very much for the information. I ran mri_surf2surf and then mris_convert to get thickness and surface area vertex wise values. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:10 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, you can use mri_surf2surf first to map them to fsaverage, then convert them to ascii On Thu, 17 Apr 2014, sabin khadka wrote: Hi Bruce, Thanks for the reply. I was wondering if I have to somehow resample or map to fsaverage so as to have same # of vertices across all subjects. I tried using mris_convert as you suggested above but I can see that different subjects have different #of vertices. Thanks for help. -Sabin On Thursday, April 17, 2014 9:29 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Sabin mris_convert can convert binary curvature format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format vertex index x y z thickness cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi Sabin mris_convert can convert binary curvature format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format vertex index x y z thickness cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin ___ 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] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
yes, you can use mri_surf2surf first to map them to fsaverage, then convert them to ascii On Thu, 17 Apr 2014, sabin khadka wrote: Hi Bruce, Thanks for the reply. I was wondering if I have to somehow resample or map to fsaverage so as to have same # of vertices across all subjects. I tried using mris_convert as you suggested above but I can see that different subjects have different #of vertices. Thanks for help. -Sabin On Thursday, April 17, 2014 9:29 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sabin mris_convert can convert binary curvature format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format vertex index x y z thickness cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin 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
Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi Bruce, Thanks for the reply. I was wondering if I have to somehow resample or map to fsaverage so as to have same # of vertices across all subjects. I tried using mris_convert as you suggested above but I can see that different subjects have different #of vertices. Thanks for help. -Sabin On Thursday, April 17, 2014 9:29 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sabin mris_convert can convert binary curvature format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format vertex index x y z thickness cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin 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.
Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi all, I ran mri_surf2surf and then mris_convert to get vertexwise thickness and surface area values in ascii files. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:30 AM, sabin khadka sabink...@yahoo.com wrote: Ahh. Great. Thanks you very much for the information. I ran mri_surf2surf and then mris_convert to get thickness and surface area vertex wise values. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:10 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, you can use mri_surf2surf first to map them to fsaverage, then convert them to ascii On Thu, 17 Apr 2014, sabin khadka wrote: Hi Bruce, Thanks for the reply. I was wondering if I have to somehow resample or map to fsaverage so as to have same # of vertices across all subjects. I tried using mris_convert as you suggested above but I can see that different subjects have different #of vertices. Thanks for help. -Sabin On Thursday, April 17, 2014 9:29 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sabin mris_convert can convert binary curvature format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format vertex index x y z thickness cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin 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.
