[Freesurfer] extracting cortical volume measures from multiple subjects

Dear FreeSurfer, I'd like to generate a spreadsheet with the cortical parcellations measures (grey matter volume, surface area) and including all subjects in my subjects directory. I seem to recall that there was a script which did this, but cannot find it in the mailing list archives. Do you rec

[Freesurfer] eTIV measures

Hi, Given the recent debate on the accuracy of the eICV in FS, I am wondering what to cite when using these measures. Do you prefer Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrov

[Freesurfer] Re: FDR correction

Dear Manja, It is statistically valid for the threshold suggested by FDR to vary in the different hemispheres. The reason is that FDR defines a proportion, not an absolute. The FDR procedure suggests a p-value threshold with the property that of all positive results at that threshold, one can expe

[Freesurfer] qdec & study-specific average

Hi, We are using our own average subject in a study, and want to use qdec. We ran recon-all -qcache -target our_study_average on all subjects in the study to make the qdec smoothed files. When I press the analyze button on the design tab, Qdec by default tries to load /surf/lh.thick.fwhm10.fs

Re: [Freesurfer] question re: p-vals and t-vals in FreeSurfer

Hi, Doug, Ok, as you point out, my conversion of p to t assumed that it was a 1-sided test. Also, I was using real data, where an effect *might* have been screwing with the outputs. I have fixed both of these problems, but my initial observation remains unchanged. Using the synthetic data, the t-

Re: [Freesurfer] question re: p-vals and t-vals in FreeSurfer

> When you do the p->t conversion, are you assuming a two-sided t? You may have spotted my silly user error... > Do you > want to try the --synth option (it's a lot easier when you *know* they > should be t). Yes. Thanks for your suggestions! +glenn > > > > [EMAIL PROTECTED] wrote: > >>Actuall

Re: [Freesurfer] question re: p-vals and t-vals in FreeSurfer

Actually, it is an excellent question, and gets at the heart of my research-- rather than saying all bets are off, using the skew of the t-values to gauge the effect (or number of hypothesis/vertices where we have an effect). My big problem is that I can't investigate the distribution of the t-val

[Freesurfer] question re: p-vals and t-vals in FreeSurfer

Hi, I'm seeing some odd behavior in t-values and p-values exported from FreeSurfer. In geeky detail: fit a linear model using FreeSurfer, saving t and p-values convert output files to ascii load ascii files into R convert the FreeSurfer "p-values" into real p-values via lh.pval <- 10^(-1*abs(free

Re: [Freesurfer] Feature request for tkmedit

As Jenni pointed out, tkmedit does ask you to save your edits when you exit using the file menu on the toolbar. I would like to see this feature extended so that it also asks when you close by clicking the x in the corner of the window. You only really need this kind of safety-check when you are t

[Freesurfer] Feature request for tkmedit

Hi, It would be great if tkmedit would ask if you have saved your edits before closing. Any chance of getting this added? As it currently stands, it is easy to just press the little x in the corner of the tkmedit window and close it, without recording any of your work. Of course no-one does this

[Freesurfer] mri_surfcluster command syntax

Hi, An oddity re: command syntax for mri_surfcluster. The --ocp flag writes the file sig.cluster.mgh. However, when I also include the --cwsig flag the file sig.cluster.mgh is not generated. Currently I run the command twice, once to generate the sig.cluster.mgh, and once to generate the cluster

[Freesurfer] cluster analysis with mri_glmfit

Hi, I have a couple of specific questions regarding cluster analysis with mri_glmfit that weren't answered at the course the other week and on which the documentation is slightly vauge. My data includes continuous variables (age and IQ, matching the documentaion!) so I should use MC simulation in

[Freesurfer] downloading freesurfer- sha1sum

Hi, yes, bundling all of the other librarys (mni, fsl, etc) with Freesurfer does make installation much easier. Thanks, team! I'm wondering if it wouldn't be too much trouble to also put up the sha1sums with the downloads? This allows a simple check that the download didn't get corrupted. I bring

[Freesurfer] determining significance levels

Hi, We've been having alot of discussion in our group regarding how one should set significance levels. Since you include FDR in the newer releases, I take it that is your current reccomendation (see also Doug's slides: http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsfsl-mris_glm.pdf). Corre