[Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

2014-03-22 Thread Pedro Rosa
Dear list, I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a structural MRI dataset and I would like to use Monte Carlo as the method for correction for multiple comparisons. However, the longitudinal LME tutorial includes only FDR correction (lme_mass_FDR2). Is it possible

Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3

2014-03-22 Thread Bruce Fischl
Hi Kim we of course always strive to make things more accurate, but in the end it will depend on the details of your acquisition and such. I don't think I have a better answer than that, other than to say look at the segmentations and see if you think they are more accurate in one case than th

Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3

2014-03-22 Thread jh kim
Dear Prof. Fischl Thanks for the prompt response. The more specific reason of my query is that there was a difference in statistical significance between two FS versions. For example, the result of group comparison of left thalamic volumes (ANCOVA controlling for age and eICV) is statistically si

Re: [Freesurfer] Difference in volumes btw 5.1 and 5,3

2014-03-22 Thread Bruce Fischl
Hi Kim there are probably lots of little reasons for the differences. This is always true for different versions, and the reason we never mix versions cheers Bruce On Sun, 23 Mar 2014, jh kim wrote: > Dear FS lists > When I measured subcortical GM volumes in the same subjects by using both > v

[Freesurfer] Difference in volumes btw 5.1 and 5,3

2014-03-22 Thread jh kim
Dear FS lists When I measured subcortical GM volumes in the same subjects by using both version 5.1 and 5.3, I have observed a considerable difference in volumes between the two versions. For instance, please see the left thalamic volumes below. I cannot figure out why there is much difference bet

Re: [Freesurfer] use 1 vs. 2 T1 acquisitions

2014-03-22 Thread Jorge Jovicich
Hello Stacey, this issue came up recently, please find attached some responses. I hope this helps. Cheers, Jorge On 21/03/2014 21:56, Stacey M Schaefer wrote: Hello freesurfer gurus, We acquire 2 BRAVO T1s on a GE 3T during the same scan session on most of our study participants, but be