Re: [Freesurfer] Surface very inaccurate after reprocessing for control points

Hi Victor, I don't think we've seen that, at least I never have. If you have a subject that this happens to can you upload it for us with the first set of control points that result in missing a lot of surface (together with the poor surfaces)? cheers Bruce On Fri, 26 Feb 2010, Laluz, Victor w

[Freesurfer] Surface very inaccurate after reprocessing for control points

Hello, Throughout most of Freesurfer's version history, I have noticed this problem pop up every 50 or so cases I do: I will have a pretty well-processed surface but with some inaccuracies in the WM surface, I will put control points down to correct it, and reprocess with autorecon2-cp as usua

Re: [Freesurfer] mri_glmfit reference

yes, that is right. doug Georg Homola wrote: > Hi, > > following these refs I've found on the list and the mri_glmfit help, I > assume the cluster-wise probability of the permutation simulation is based > on cluster mass inference, is that right? > > Thanks, > Georg > > > Statistical Science 200

Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor

You can specify that there are 4 trial types (AA, AB, BA, BB), and give the duration twice that of the individual. doug Gaber, Tilman wrote: > Dear mailinglist recipients, > > I am currently planning an optimized experiment using optseq2 and a 2x2 > factors behavioral response task (Simon-task

Re: [Freesurfer] Gaussian Curvature Calculation

Yes -- that's exactly right. The '--discrete' is also the default so doesn't need to be specified. The '--continuous' uses the old curvature engine. You will notice that each engine option results in slightly different curvature values. Sent via BlackBerry from T-Mobile -Original Message

[Freesurfer] how to use time points

Hi, there, I have scans from two time points, and they have been cross-sectionally processed. But both of they missed some white matter in some slices, so I manually add control points to them, and re-run it. Both of them look fine now. Then, I send them to longitudinal stream. After the -ba

Re: [Freesurfer] Gaussian Curvature Calculation

not sure about --continuous, Rudolph will know. The quadratic patch stuff is in mris_cuvature, but maybe also in mris_curvature_stats On Fri, 26 Feb 2010, Lisa Ronan wrote: > Many thanks for that. Am I correct in thinking that the Gauss_Bonnet scheme > is given by the "--discrete" option in mris

Re: [Freesurfer] Gaussian Curvature Calculation

Many thanks for that. Am I correct in thinking that the Gauss_Bonnet scheme is given by the "--discrete" option in mris_curvature_stats, while the latter option is given by the "--continuous" flag? L On Fri, Feb 26, 2010 at 1:46 PM, Bruce Fischl wrote: > Hi Lisa, > > we actually provide a discr

Re: [Freesurfer] How to verify cerebellum segmentation

Hi Gergely, overlay the aseg.mgz on the norm.mgz in tkmedit and you can visually verify if it's accurate. If not, you can edit it with the tools in tkmedit. We do have some internal tools for VBM-style analysis but rarely use them as the results are so ambiguous. It should be easy enough to stu

Re: [Freesurfer] Gaussian Curvature Calculation

Hi Lisa, we actually provide a discrete estimate using Gauss-Bonnet (Rudolph can give you the details), and a slightly larger-scale estimate by fitting a quadratic patch to each neighborhood (5mm on a side I think). The curvature then comes from the Hessian of the height function of that patch.

[Freesurfer] How to verify cerebellum segmentation

Hi all! We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower int

[Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor

Dear mailinglist recipients, I am currently planning an optimized experiment using optseq2 and a 2x2 factors behavioral response task (Simon-task). The task consists of a pseudo-randomized series of two kinds of trials (congruent and incongruent). In addition there is a sequential factor, i.e.

[Freesurfer] Gaussian Curvature Calculation

Hi All I wonder could you tell me how Gaussian curvature values are computed at a vertex, i.e. Gauss_Bonnet scheme? Is there any way to vary the neighborhood over which the vertex curvature values are computed? Thanks for your help, Lisa Ronan - - - - - - - - - - Research Associate Brain Mappi

Re: [Freesurfer] ICV Error fs 4.3.1

Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I