Re: [Freesurfer] A question regarding DODS or DOSS

2014-02-02 Thread KimMJ
Dear Doug and Donald Thank you for your kind directions. 1) When I perform DOSS using the contrast (1 -1 0), the significant areas of cortical thinning in patients relative to controls (i.e., temporo-occipital cortex) were similar but more widespread in comparison with those in DODS analysis

Re: [Freesurfer] Significant cluster only shows up in the terminal but not on the template brain

2014-02-02 Thread Tudor Popescu
Hi Marie, Ah yes, thanks, that was indeed the problem! Strangely though, the Max for that cluster is t=2.488 initially, above the default t=2 Min value in the QDEC visualisation settings! But after pressing the FindClusters button, Max becomes t=1.779 and so the Min probably needs to be lowered i

Re: [Freesurfer] Significant cluster only shows up in the terminal but not on the template brain

2014-02-02 Thread Marie Schaer
Hi Tudor, Seems to me that it could be just a display issue, as you didn't adjust the visualisation threshold (you have min = 2), whereas you run your Monte Carlo with a threshold of 0.05 (i.e. 1.3), and your cluster seem to be just in between. Hope it helps, Marie On Feb 2, 2014, at 10:55

[Freesurfer] TRACULA -stat

2014-02-02 Thread stdp82
Normal 0 false false false IT JA X-NONE

[Freesurfer] from label to mask diffusion space

2014-02-02 Thread Garikoitz Lerma-Usabiaga
Hi Doug, I've been reading the list and I ended with 4 steps to move from a label to a mask in diffusion space (below). Is this correct? Is there any other more straightforward way? It should end with a binary mask in diffusion space (I am using the anatorig2diff.bbr.dat created in the Tracula proc