use tkmedit or freeview
On 12/07/2016 07:43 AM, Hao wen wrote: > > Thanks for your advice, > > After I got 'out.mgz', I know for aparc.annot, pysurfer use tksurfer > to visualize the map, but for aseg.annot, because it is volume_based > analysis, I want to have some thing like this, which has been down in > freeview to display the segmentation output of recon-alll output: > > > > But the different colors for the subcortical regions will be the > correspondent z-value for two groups, so what do you think if we can > make it by tksurfer, tkmedit or freeview?? > Thanks very much > ------------------------------------------------------------------------ > *De :* [email protected] > <[email protected]> de la part de Douglas N Greve > <[email protected]> > *Envoyé :* mardi 6 décembre 2016 23:21 > *À :* [email protected] > *Objet :* Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale > result to plot a z-score map for the segmentation > That is a little easier. In matlab you can > > seg = MRIread('youseg.mgz'); > > out = seg; > > out.vol = zeros(size(out.vol)); > > ind = find(seg.vol == segno); > > out.vol(ind) = valueforsegno; > > MRIwrite(out,'out.mgz'); > > > > On 12/06/2016 05:04 PM, Hao wen wrote: > > > > > > Hello, I checked your script, I think this is to map the aparc.annot, > > I have already done that, what I want is to map the aseg.annot > > subcortical segmentation like what we can do for aparc, so do you have > > any idea?? > > Thanks in advance > > > > ------------------------------------------------------------------------ > > *De :* Hao wen > > *Envoyé :* mardi 6 décembre 2016 18:18 > > *À :* [email protected] > > *Objet :* RE: [Freesurfer] Volumetric Group Analysis: asegstats2tbale > > result to plot a z-score map for the segmentation > > > > Thanks very much, I will try to look at that:) > > > > Perfect FS,hahah > > > > > > > > ------------------------------------------------------------------------ > > *De :* [email protected] > > <[email protected]> de la part de Douglas Greve > > <[email protected]> > > *Envoyé :* mardi 6 décembre 2016 17:51 > > *À :* [email protected] > > *Objet :* Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale > > result to plot a z-score map for the segmentation > > > > This is a tricky thing to do. I've created a matlab file to help, > > which you can get from here: > > > > > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m > > > > > > Look at the help for an example on how to use it. You will have to > > specify the list of ROI names and the corresponding list of values > > that you want each ROI to be filled with. See the example > > > > > > > > On 12/6/16 9:57 AM, Hao wen wrote: > >> > >> Hello, FS experts: > >> > >> I have a question for visualizing statistical analysis > >> asegstats2tbale result into a map like what we have done in qdec, > >> which uses the thickness information, so if i want to use the volume > >> information of the different segmentation volume, and after doing > >> z-score for two groups, how can I visualize it into a z map??? > >> > >> For example, for the volumetric group analysis, I compute the > >> z-scores for the different subcortical volumes between these two > >> group, how do i visualize the result in sphere??? > >> > >> > >> Really need your help > >> > >> Any help will be appreciated > >> > >> Hao > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> [email protected] > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Freesurfer Info Page - Harvard University > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > mail.nmr.mgh.harvard.edu > To see the collection of prior postings to the list, visit the > Freesurfer Archives. A searchable archive which of messages PRIOR to > March 2004 is at ... > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Freesurfer Info Page - Harvard University > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > mail.nmr.mgh.harvard.edu > To see the collection of prior postings to the list, visit the > Freesurfer Archives. A searchable archive which of messages PRIOR to > March 2004 is at ... > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > FileDrop v2.0 - Martinos Center for Biomedical Imaging > <https://gate.nmr.mgh.harvard.edu/filedrop2> > gate.nmr.mgh.harvard.edu > Filedrop is for sending files work-related files up to 2GiB; For files > over 2GiB, please use the Accellion File Transfer from Partners; > Filedrop is not a secure ... > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Martinos Center File Drop > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > www.nmr.mgh.harvard.edu > 11/15/2012 -- There is a new version of Filedrop. Please help us test > it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos > Center file drop area. > > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
