Re: [Freesurfer] Thickness values to a common space
Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ 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.
Re: [Freesurfer] Thickness values to a common space
what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- 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] Thickness values to a common space
Hi Doug, Thanks for the reply. Those are the two steps I followed to extract vertexwise surface area, thickness and pial_lgi values Step 1: mri_surf2surf --hemi ?h --srcsubject SUB001 [thickness, area or pial_lgi] --src_type curv --trgsubject fsaverage --trgsurfval SUB001-area --trg_type curv Step 2: mris_convert -c SUB001-area ?h.white SUB001-area.asc Can you direct me on how to get vertex wise thickness, surface area and pial_lgi values for a subject and extract in a ascii file. And also, if I want to convert ascii file with thickness values to freesurfer format, how would I do it? Thanks, Sabin On Tuesday, April 15, 2014 11:29 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- 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___ 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] Thickness values to a common space
Can you send the exact command line you are using (no wildcards or substitutions) and the terminal output that you get? On 04/15/2014 11:52 AM, sabin khadka wrote: Hi Doug, Thanks for the reply. Those are the two steps I followed to extract vertexwise surface area, thickness and pial_lgi values Step 1: mri_surf2surf --hemi ?h --srcsubject SUB001 [thickness, area or pial_lgi] --src_type curv --trgsubject fsaverage --trgsurfval SUB001-area --trg_type curv Step 2: mris_convert -c SUB001-area ?h.white SUB001-area.asc Can you direct me on how to get vertex wise thickness, surface area and pial_lgi values for a subject and extract in a ascii file. And also, if I want to convert ascii file with thickness values to freesurfer format, how would I do it? Thanks, Sabin On Tuesday, April 15, 2014 11:29 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu mailto:whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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 mailto: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 -- 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
[Freesurfer] Thickness values to a common space
I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ 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.
