Hi All,
mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf).
Thank you very much in advance for your help!
All the best,
Ruthger
Hi Ruthger!
Use mris_expand to create a surf inside or outside of white
e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white
Cheers! Markus
2014-04-03 16:24 GMT+02:00 Righart, Ruthger righart@lrz.tu-muenchen.de:
Hi All,
mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf).
Thank you very much in advance for your help!
All the best,
Ruthger _______________________________________________ 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.
Hi Markus, Thank you, excellent tool and gives exactly what I was searching for! Is the resulting surface the same for mris_expand taken at 50% as the one that is used in mri_vol2surf with flag projfrac 0.5? I wondered if something is done differently as processing time for mris_expand is much longer (at about 14 min.) as compared with mri_vol2surf (couple of minutes). Any ideas on this would be welcome! Ruthger
Le 2014-04-03 16:39, Markus Gschwind a écrit :
Hi Ruthger!
Use mris_expand to create a surf inside or outside of white
e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white
Cheers! Markus
2014-04-03 16:24 GMT+02:00 Righart, Ruthger righart@lrz.tu-muenchen.de:
Hi All,
mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [1]).
Thank you very much in advance for your help!
All the best,
Ruthger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2]
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 [3] . 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.
Links:
[1] http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [3] http://www.partners.org/complianceline
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.
Hi Ruthger
no, they are not the same. mris_expand generates a smooth non-self-intersecting surface, which is definitely not guaranteed by simple projection.
cheers Bruce On Fri, 4 Apr 2014, Righart, Ruthger wrote:
Hi Markus, Thank you, excellent tool and gives exactly what I was searching for! Is the resulting surface the same for mris_expand taken at 50% as the one that is used in mri_vol2surf with flag projfrac 0.5? I wondered if something is done differently as processing time for mris_expand is much longer (at about 14 min.) as compared with mri_vol2surf (couple of minutes). Any ideas on this would be welcome! Ruthger
Le 2014-04-03 16:39, Markus Gschwind a écrit :
Hi Ruthger!
Use mris_expand to create a surf inside or outside of white
e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white
Cheers! Markus
2014-04-03 16:24 GMT+02:00 Righart, Ruthger righart@lrz.tu-muenchen.de:
Hi All,
mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [1]).
Thank you very much in advance for your help!
All the best,
Ruthger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2]
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 [3] . 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.
Links:
[1] http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [3] http://www.partners.org/complianceline
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
They are not exactly the same. However, if you run mri_vol2surf with --surf white50 --projfrac 0 it will be identical (where white50 is the surface create with mris_expand)
doug
On 04/04/2014 05:34 AM, Righart, Ruthger wrote:
Hi Markus, Thank you, excellent tool and gives exactly what I was searching for! Is the resulting surface the same for mris_expand taken at 50% as the one that is used in mri_vol2surf with flag projfrac 0.5? I wondered if something is done differently as processing time for mris_expand is much longer (at about 14 min.) as compared with mri_vol2surf (couple of minutes). Any ideas on this would be welcome! Ruthger
Le 2014-04-03 16:39, Markus Gschwind a écrit :
Hi Ruthger!
Use mris_expand to create a surf inside or outside of white
e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white
Cheers! Markus
2014-04-03 16:24 GMT+02:00 Righart, Ruthger righart@lrz.tu-muenchen.de:
Hi All,
mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [1]).
Thank you very much in advance for your help!
All the best,
Ruthger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [2]
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 [3] . 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.
Links:
[1] http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf [2] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [3] http://www.partners.org/complianceline
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Markus Gschwind -
Righart, Ruthger