That is the "fill threshold". It indicates how many label points must fall into a voxel in order for that voxel to be considered part of the label. By default it is just over 0, meaning that even one label point falling into the voxel will make that voxel labeled. I would leave it like, look at the mask, and then reduce it if you want the mask to be a little bit smaller. doug
Zhangyuanchao wrote: > Hi,doug, > > In the help page of mri_label2vol, I see the following information as > an example of the usage of this command: > > 2. Convert a surface label into a binary mask in the functional space. > Fill in all the cortical gray matter. Require that a functional voxel > be filled at least 30% by the label: > mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii > --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject > bert --hemi lh --o cent-lh.nii > > I noticed the option of fillthresh,I do not quite understand what is > the meaning of the parameter of fillthresh, whose default value is 0; > In your last email, you omit this option to use the default value. > I wonder whether this is too loose a threshold given that the > resolution of functional images are low. Is it possible that the > obtained mask contains voxels which are not gray matter? > I am not sure, I want to use this mask as seed region for further > analysis. Could you show me how to choose the correct threshold of the > fillthresh option? > > Thanks a lot for your kindness and patiency! > > Yuanchao > > --- *11年12月14日，周三, Douglas N Greve > /<gr...@nmr.mgh.harvard.edu>/* 写道： > > > 发件人: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > 主题: Re: [Freesurfer] convert surface label on to functional image > 收件人: "Zhangyuanchao" <woshizhan...@yahoo.cn>, "freesurfer" > <freesurfer@nmr.mgh.harvard.edu> > 日期: 2011年12月14日,周三,上午1:01 > > The easiest thing is to use mri_label2vol, something like > mri_label2vol --label yourlabel.label --temp functemplate.nii --reg > register.dat --proj frac 0 1 .1 --hemi lh --subject subject --o > yourlabel.nii > > doug > > Zhangyuanchao wrote: > > Thanks for your response! > > > > In fact, the label that I want to convert to functional space was > > obtained by between-group comparisons, so it does not belong to any > > existing parcellation template. > > > > What should I do in this case? > > > > Thanks! > > > > Best, > > > > --- *11年12月13日，周二, Douglas N Greve > > /<gr...@nmr.mgh.harvard.edu > </mc/compose?to=gr...@nmr.mgh.harvard.edu>>/* 写道： > > > > > > 发件人: Douglas N Greve <gr...@nmr.mgh.harvard.edu > </mc/compose?to=gr...@nmr.mgh.harvard.edu>> > > 主题: Re: [Freesurfer] convert surface label on to > functional image > > 收件人: "Zhangyuanchao" <woshizhan...@yahoo.cn > </mc/compose?to=woshizhan...@yahoo.cn>> > > 抄送: freesurfer@nmr.mgh.harvard.edu > </mc/compose?to=freesurfer@nmr.mgh.harvard.edu> > > 日期: 2011年12月13日,周二,上午5:48 > > > > Hi Yuanchao, I would recommend that you use the aparc+aseg.mgz > > file for this. This file has cortical labels already in the > > volume, you just need to map them to your functional space, > > something like > > > > mri_label2vol --aparc+aseg --temp functemplate.nii --reg > > register.dat --o aparc+aseg.fmri.nii > > > > doug > > > > Zhangyuanchao wrote: > > > hi, expert, > > > > > > By mapping a surface label to a functional template, I want to > > extract the corresponding cortical gray matter region in the > > functional space. I know I should use the mri_label2vol command. > > > In the help page of mri_label2vol, I see some examples of this > > command. > > > > > > 2. Convert a surface label into a binary mask in the > functional > > space. > > > Fill in all the cortical gray matter. Require that a > functional > > voxel > > > be filled at least 30% by the label: > > > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > > f.nii --reg register.dat --fillthresh .3 --proj frac 0 1 > > .1 --subject bert --hemi lh > > > --o cent-lh.nii > > > > > > 3. Convert a surface label into a binary mask in the > functional > > space. > > > Sample a 1mm ribbon 2mm below the gray/white surface. Do not > > require a fill threshold: > > > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > > f.nii --reg register.dat --proj abs -3 -2 .1 --subject > bert > > --hemi lh > > > --o cent-lh.nii > > > > > > I want to extract the cortical gray matter on the functional > > images corresponding to the surface label. I do not know > which of > > the above commands could obtain the result I want and which > > parameters I should use to obtain what I want. > > > > > > For example 3, I do not quite catch what "Sample a 1mm ribbon > > 2mm below the gray/white surface. " this sentence means. > > > Thanks for your help! > > > > > > > > > Best > > > > > > Yuanchao > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > </mc/compose?to=Freesurfer@nmr.mgh.harvard.edu> > > </mc/compose?to=Freesurfer@nmr.mgh.harvard.edu > </mc/compose?to=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 > </mc/compose?to=gr...@nmr.mgh.harvard.edu> > </mc/compose?to=gr...@nmr.mgh.harvard.edu > </mc/compose?to=gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > 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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu </mc/compose?to=gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
