[Freesurfer] Is there any way to measure the volume of substantia nigra and red nucleus via FS?

Hi, FreeSurfer experts, I would like to know is there any command to measure the volume of substantia nigra, red nucleus, and anyother nucleis in brainstem by using FS ? Thanks in advance, Nellie___ Freesurfer mailing list

[Freesurfer] QDEC_ information extraction

Dear Freesurfer Experts, Sorry to bother the mailing list again, but I really confused with the information extraction of significant clusters from QDEC. Basically, there were two main questions: (1)I have knew that the stimulation output summary was named “mc-z.abs.th20.sig.cluster.summary”

[Freesurfer] problems on matrix design

Hi Freesurfer Experts,I have tried to alter wiki example FSGD table into my analyses these days, according to your advice, but there are still some problems. Supposed there are 6 groups (maleclass1, maleclass2, maleclass3, femaleclass1, femaleclass2, femaleclass3) and 2 Variables (age,

[Freesurfer] Still unsure how to create my 3g4v matrix

text/plain; charset="iso-8859-7" > >Hi Li, > >You can find some example FSGD tables here, which you can alter to fit your >analyses. > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >Best, >Lee > >On Sun, 22 Nov 2015, nellie wrote: > >

Re: [Freesurfer] How to create a 3g4v matrix

text/plain; charset="iso-8859-7" > >Hi Li, > >You can find some example FSGD tables here, which you can alter to fit your >analyses. > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >Best, >Lee > >On Sun, 22 Nov 2015, nellie wrote: > >

[Freesurfer] How to create a 3g4v matrix

Hi Freesurfer Experts, I’m a new user of Freesurfer, and I learn how to use this software mainly through Wiki. When I came to the step of using GLM to compare group differences, I was confused on the design of 3g4v matrix. In my study, there were 3 classes (A / B / C group) and 4 concomitant

[Freesurfer] How to create a FSGD file

Dear Freesurfer engineers, According to the introduction of Wiki, I know the exact structure of a legal FSGD file. However, I still don't know how to create a FSGD file, for example, using which command or through which way to create it? Hoping for your reply. Thanks a lot ! Best wishes,

Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 26

Dear Lee,Greatly appreciate for your advice. But I not sure whether it is the reason for the comand killed. Actually, I had used the method, useing the -i flag for each .dcm file for your training data of “014-anon” and then running the comand “recon-all -s 014-anon -all”, to get a final