Re: [Freesurfer] mis-registartion question

2019-06-28 Thread Nasiriavanaki, Zahra
I guess what I’m concerned about is the high values of tkregister-sess even though the registration looks normal. I have checked tkregister values in other subjects with the same slab of functional data, and their values are within the normal range (~0.2-0.3), but for this subject the values of

[Freesurfer] total cortical area

2019-06-28 Thread Barletta, Valeria
Dear Freesurfers, Where in the /mri/stats folder can I find the total cortical surface in mm2? Is it in the ?h.aparc.stats or in the ?h.curv.stats? Thank you, Valeria ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

[Freesurfer] How to account for gender in a contrast matrix

2019-06-28 Thread Basavaraju, Rakshathi
External Email - Use Caution Dear all FS users, I wanted to know the way of accounting for gender in a simple regression analysis of cortical thickness against 2 continuous variables. Th example of contrast matrix given in the downloaded tutorial data for cortical thickness with

Re: [Freesurfer] Freesurfer linear mixed models - viewing results {Disarmed}

2019-06-28 Thread Mark Wagshul
External Email - Use Caution Thanks. Yes, we understand that, and now have the model significance maps to look at. But, just to be clear: once we have exported the significance (or beta) maps using fs_write_Y, we should be able to open up this object as a surface, correct? Ou

Re: [Freesurfer] Longitudinal Masking and FDR

2019-06-28 Thread Diers, Kersten /DZNE
External Email - Use Caution Hello Jessica, the FDR2 threshold is computed by means of a two-step procedure, and it depends on the actual p-values that one supplies as input to the script. In a scenario where no p-value survives the initial (step 1) threshold that is computed w

[Freesurfer] [Updated announcement] Postdoc position opening at Brown University in cognitive aging and Alzheimer’s disease

2019-06-28 Thread Hwamee Oh
External Email - Use Caution We are seeking a highly motivated postdoctoral researcher to study behavioral and neuroimaging markers of preclinical Alzheimer’s disease in the Warren Alpert Medical School of Brown University. The primary performance site for this postdoctoral fellows

Re: [Freesurfer] Area information on certain views

2019-06-28 Thread Greve, Douglas N.,Ph.D.
You mean the cross sectional area? I don't think we have tools to do that, though you might be able to do it in matlab. On 6/27/2019 11:02 PM, Kim, Jisoo,M.D. wrote: Dear freesurfer team, I searched the archives, but couldn't find this kind of question. I've used the brainstem segmentation