Dear experts, Before I get the reply, I want to give more background and clarify my question:
My label ROIs is not getting from the structural data. My label ROIs is some visual areas which I mannually got after I did the retinotopic mapping analysis: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. Because in that analysis, the functional data is registered to the "self"(preproc-sess -surface self) which was from recon-all, I simply mentioned the ROIs were from recon-all results in last email. Actually, I really want to know which data (mri/brain.mgz? or mri/rawavg.mgz or T1.mgz? ) the retinotopic data is registered to by "-surface self". To my understanding, the data (the retinotopic data is registered to) should be the template (by --temp) of mri_label2vol, right? And, the register.dat is getting by register the volume used in FSL for further analysis to that data? Thanks in advance! Mingxia Zhang On Sun, Jun 7, 2015 at 4:13 PM, zhang mingxia <zhangmingxia1...@gmail.com> wrote: > Dear experts, > > I saw a lot of people have posted this issue, but it's not exactly the > same as what I met. Hopefully some one would reply me. > > What I have done is running recon-all on each subject's structural data > and manually getting some labels as the ROIs. My further analysis is > extract the value of these ROIs from the functional data which has been > preprocessed by FSL. > > Now, the label ROIs was abtained from each subject(not the average brain > but indivisual's space) and the final volumetric masks should also be in > individual's space. So, my question is, how to convert these label ROIs > into volumetric ROIs(both in individual's space)? > > What i am going to do is using mri_label2vol to do it. But it's very good > to verify some options. For example, for label1(rh) of subject01(s01), I am > going to use the command below: > > mri_label2vol --label label1.label --temp s01/mri/rawavg.mgz --subject s01 > --hemi rh --o label1.nii.gz --proj frac 0 1 .1 --fillthresh .3 –reg > register.dat > > (1)I can generally understand register.dat is the matrix of registering > the surface to volume(or volume to surface?), but how exactly does this > metrix produce? For example, the functinal data of s01 is func.nii.gz, what > command should I use? > > (2)Is it correct for rawavg.mgz to be template? Is it correct for > fillthresh to be 0.3? > > Any reply are really appreciated! > > Mingxia Zhang > > >
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