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.
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 whatsdac@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.
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.
- 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 whatsdac@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
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 greve@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.
- 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 whatsdac@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
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 greve@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.
- 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 <whatsdac@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.
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