hello
we are trying to project a vector of results for segmented cortical regions (i.e., ... "lh_middletemporal_thickness" 0.000757119 "rh_middletemporal_thickness" 8.06E-05 "lh_parahippocampal_thickness" -0.000510407 "rh_parahippocampal_thickness" 0.000625997 "lh_pericalcarine_thickness" 0.000499749 "rh_pericalcarine_thickness" 0.000903678 "lh_superiortemporal_thickness" 0.001732855 "rh_superiortemporal_thickness" 0.000184256 "lh_temporalpole_thickness" 0.001075362 "rh_temporalpole_thickness" -0.000381165 "lh_transversetemporal_thickness" 0.000558122 "rh_transversetemporal_thickness" 6.65E-05 ...)
however, we are unsure of how to do this. so, our question is— what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer.
Thanks for your help,
Brian Weisinger
Hi Brian,
I guess you can use read_annotation.m in matlab and set every vertex within the given parcellation to the value you specify below, then write it out as either an nvertices x 1 x 1 .mgz file with save_mgh, or use write_curv.m
cheers Bruce
On Mon, 28 Nov 2011, Weisinger, Brian (NIH/NIMH) [F] wrote:
hello
we are trying to project a vector of results for segmented cortical regions (i.e., ... "lh_middletemporal_thickness" 0.000757119 "rh_middletemporal_thickness" 8.06E-05 "lh_parahippocampal_thickness" -0.000510407 "rh_parahippocampal_thickness" 0.000625997 "lh_pericalcarine_thickness" 0.000499749 "rh_pericalcarine_thickness" 0.000903678 "lh_superiortemporal_thickness" 0.001732855 "rh_superiortemporal_thickness" 0.000184256 "lh_temporalpole_thickness" 0.001075362 "rh_temporalpole_thickness" -0.000381165 "lh_transversetemporal_thickness" 0.000558122 "rh_transversetemporal_thickness" 6.65E-05 ...)
however, we are unsure of how to do this. so, our question is? what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer.
Thanks for your help,
Brian Weisinger
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the help. We don't have matlab here in our lab, but we do have R. Is there a way to use R and get the same desired result?
On 11/28/11 11:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Brian,
I guess you can use read_annotation.m in matlab and set every vertex within the given parcellation to the value you specify below, then write it out as either an nvertices x 1 x 1 .mgz file with save_mgh, or use write_curv.m
cheers Bruce
On Mon, 28 Nov 2011, Weisinger, Brian (NIH/NIMH) [F] wrote:
hello
we are trying to project a vector of results for segmented cortical regions (i.e., ... "lh_middletemporal_thickness" 0.000757119 "rh_middletemporal_thickness" 8.06E-05 "lh_parahippocampal_thickness" -0.000510407 "rh_parahippocampal_thickness" 0.000625997 "lh_pericalcarine_thickness" 0.000499749 "rh_pericalcarine_thickness" 0.000903678 "lh_superiortemporal_thickness" 0.001732855 "rh_superiortemporal_thickness" 0.000184256 "lh_temporalpole_thickness" 0.001075362 "rh_temporalpole_thickness" -0.000381165 "lh_transversetemporal_thickness" 0.000558122 "rh_transversetemporal_thickness" 6.65E-05 ...)
however, we are unsure of how to do this. so, our question is? what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer.
Thanks for your help,
Brian Weisinger
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.
If you've got any Python users in the lab, this shouldn't be to hard to accomplish with pysurfer: pysurfer.github.com
I'm happy to walk you through the steps if you're interested.
Michael
On Mon, Nov 28, 2011 at 8:52 AM, Weisinger, Brian (NIH/NIMH) [F] < brian.weisinger@nih.gov> wrote:
Thanks for the help. We don't have matlab here in our lab, but we do have R. Is there a way to use R and get the same desired result?
On 11/28/11 11:46 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Brian,
I guess you can use read_annotation.m in matlab and set every vertex within the given parcellation to the value you specify below, then write it out as either an nvertices x 1 x 1 .mgz file with save_mgh, or use write_curv.m
cheers Bruce
On Mon, 28 Nov 2011, Weisinger, Brian (NIH/NIMH) [F] wrote:
hello
we are trying to project a vector of results for segmented cortical
regions
(i.e., ... "lh_middletemporal_thickness" 0.000757119 "rh_middletemporal_thickness" 8.06E-05 "lh_parahippocampal_thickness" -0.000510407 "rh_parahippocampal_thickness" 0.000625997 "lh_pericalcarine_thickness" 0.000499749 "rh_pericalcarine_thickness" 0.000903678 "lh_superiortemporal_thickness" 0.001732855 "rh_superiortemporal_thickness" 0.000184256 "lh_temporalpole_thickness" 0.001075362 "rh_temporalpole_thickness" -0.000381165 "lh_transversetemporal_thickness" 0.000558122 "rh_transversetemporal_thickness" 6.65E-05 ...)
however, we are unsure of how to do this. so, our question is? what is the sequence of steps we need to take to
visualize our results on the segmented 3D template in tksurfer.
Thanks for your help,
Brian Weisinger
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
This is not a super easy thing to do, but it is possible if you have matlab. First, go to the subject's surf directory and run mri_convert lh.thickness lh.template.mgh This just creates a template that can be loaded into matlab. Load the aparc.annot into matlab with read_annotation.m. Load the template with t = MRIread('lh.template.mgh'); t.vol = zeros(t.volsize); % make sure all values are 0 Find the indices in label that match middletemporal, and set them to your target value in t.vol: t.vol(indices) = 0.000757119; Do this for all of your ROIs Then write out the structure with MRIwrite(t,'youdata.mgh'); You an then view it with tksurfer with tksurfer subject lh inflated -aparc -overlay yourdata.mgh
doug
Weisinger, Brian (NIH/NIMH) [F] wrote:
hello
we are trying to project a vector of results for segmented cortical regions (i.e., ... "lh_middletemporal_thickness" 0.000757119 "rh_middletemporal_thickness" 8.06E-05 "lh_parahippocampal_thickness" -0.000510407 "rh_parahippocampal_thickness" 0.000625997 "lh_pericalcarine_thickness" 0.000499749 "rh_pericalcarine_thickness" 0.000903678 "lh_superiortemporal_thickness" 0.001732855 "rh_superiortemporal_thickness" 0.000184256 "lh_temporalpole_thickness" 0.001075362 "rh_temporalpole_thickness" -0.000381165 "lh_transversetemporal_thickness" 0.000558122 "rh_transversetemporal_thickness" 6.65E-05 ...)
however, we are unsure of how to do this. so, our question is— what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer.
Thanks for your help,
Brian Weisinger
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Michael Waskom -
Weisinger, Brian (NIH/NIMH) [F]