Re: [Freesurfer] Qdec - ROI - different thickness results

2011-02-28 Thread Alex Hanganu
Thank you very much for the idea Nick, this explained everything. In qdec red means XY we didn't notice the thickness data on that plot at first :( Have a wonderful week ! Sincerely, Alex. --- En date de : Dim 27.2.11, Nick Schmansky ni...@nmr.mgh.harvard.edu a écrit : De: Nick Schmansky

[Freesurfer] Postdoctoral Fellowship in multimodal developmental neuroimaging

2011-02-28 Thread Michels Lars
Applications are invited for an 18 month postdoctoral fellowship in the human multimodal neuroimaging project Linking the major system markers for typical and atypical brain development: a multimodal imaging and spectroscopy study (http://www.zihp.uzh.ch/1610.php#45) funded by the Zürich

[Freesurfer] residuals exactly zero

2011-02-28 Thread Lars M. Rimol
Hi, We have experimented a little with different ways of computing the p-values in a GLM analysis based on FreeSurfer data. The way the Matlab reference implementation (fast_fratio.m) handles a situtation where the residuals are exactly zero, seems to be to set those vertices to F = 0 and p = 1.

Re: [Freesurfer] residuals exactly zero

2011-02-28 Thread Douglas N Greve
When the residual variance is exactly 0, this is what the matlab code. In the C implementation, if (glm-rvar FLT_MIN) glm-rvar = FLT_MIN; which will have similar results. doug Lars M. Rimol wrote: Hi, We have experimented a little with different ways of computing the p-values in a GLM

[Freesurfer] Baseline Offset in Stable 5 funcroi

2011-02-28 Thread Adam Nitenson
Hi Freesurfers, When conducting ROI analyses in Stable 5, is there a way to generate a mean functional baseline offset value within the ROI which can be used to help calculate percent signal change? This would correspond to the value from row 4 in the output file generated by

Re: [Freesurfer] thickness analyse

2011-02-28 Thread Nick Schmansky
wang, i think having the imported roi thickness data in your qdec.table.dat file is confusing you. you should just delete that data from your qdec.table.dat, keeping just 'fsid' and 'addiction' columns. from looking at your analysis (which appears you have done everything right), it is not used

Re: [Freesurfer] win xp shared drives

2011-02-28 Thread Saad Ramadan
Hi, I have recently installed freesurfer 5.0.0 on top of a Xubuntu Linux distribution on an virtualBox/WIN XP computer. I can run freesurfer without a problem. My problem is with accessing Host drives from linux system. How am I going to get the image data to my linux virtual system if I cannot

Re: [Freesurfer] win xp shared drives

2011-02-28 Thread Nick Schmansky
saad, i dont have the information directly on-hand, but in your virtual box configuration (independent of freesurfer) there should be an option to map a USB drive into the linux virtual machine. others have done this successfully. you'd have to google the help docs for your virtual box to learn

[Freesurfer] NIFTI-2 public announcement

2011-02-28 Thread Douglas N Greve
FYI _* _* _* _* _*A 64-bit update to the NIfTI format*_ *_ *_ *_ *_ The NIfTI committee are proposing the creation of a NIfTI-2 format that is a very simple extension of the current NIfTI-1 format, but updated to allow 64-bit storage and addressing for large images and matrices. _ _ It is