Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

Hi Cecilio what do you mean 224 scans? I assume you mean 224 slices in each scan? And do you have two different runs of the same scan type (e.g. mprage) for each subject? You can try: mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 and freeview

[Freesurfer] Tracula data and ICV

Dear Anastasia: Hope all is well. I have done tracula analysis on 75 brains (HARDI) and I am statistically analyzing the data. Do I need to use ICV as a covariate in my statistical model? thank you, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD*

Re: [Freesurfer] Recon all exited with error

Hi Hassan you need to look at the lh.orig.nofix and the lh.inflated.nofix to see what is going on. Typically this happens if there is some massive topological defect caused by e.g. the skull or cerebellum being attached to the wm. cheers Bruce On Sat, 25 Apr 2015, Hassan bakhshi wrote:

Re: [Freesurfer] Reconall not properly parcellating brain

Hi Rachel what do you mean that it's a screenshot of talairach.xfm? Did you apply the transform to this volume? The bright spot is some cause for concern and probably is why stuff was excluded. Can you look back through your data and see where the bright patch first appears (rawavg.mgz?