[Freesurfer] Freesurfer projecting vector results for segmented cortical regions
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.
Re: [Freesurfer] Freesurfer projecting vector results for segmented cortical regions
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 > > > ___ 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] Freesurfer projecting vector results for segmented cortical regions
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" 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
Re: [Freesurfer] Freesurfer projecting vector results for segmented cortical regions
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.weisin...@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" 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 > ___ 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] Freesurfer projecting vector results for segmented cortical regions
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
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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___
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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
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