Re: [Freesurfer] anatomical stats in stable-pub-v3.0.5

Hi Paul, the mris_volume method probably includes hippocampus and amygdala, which mris_anatomical_stats should remove, although the difference you are seeing goes in the other direction, which I don't understand. Bruce On Fri, 21 Dec 2007, Paul Greenberg wrote: Hi All, I've processed a se

[Freesurfer] anatomical stats in stable-pub-v3.0.5

Hi All, I've processed a set of 40 subjects with freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 and am now working on a series of morphometric analyses. I am comparing gray matter volumes found in: 1) aparc.stats from recon-all, (same as output of "mris_anatomical_stats" run from the comm

Re: [Freesurfer] Cerebellar surface?

Hi Paul, I don't think you can get good cerebellar surfaces without significantly higher resolution, otherwise you lose all the foliations. There are some plans afoot to generate a volumetric lobar parcellation cheers, Bruce On Fri, 21 Dec 2007, Paul Greenberg wrote: Hi all, Are there a

Re: [Freesurfer] Cluster thresholding

Thanks Pratap and Cameron. When I said primary cluster forming threshold, I did mean the vertex-wise p-value. I imagine it should be reported, as it will affect the clusters you subsequently extract (lower p-values would lead to larger clusters needed for significance (??)). Does anyone have any

[Freesurfer] Cerebellar surface?

Hi all, Are there any plans for freesurfer to create a cerebellar surface rendering suitable for the display of fMRI results, or is 3D Slicer a good option for creating a 3D cerebellum from the aseg parcellation? Thanks much and happy holidays, Paul -- Paul Greenberg, Ph.D. Radiology Depart

Re: [Freesurfer] jacobian analyses

Hi Mike, we should probably rerun mris_jacobian at the end with ?h.white as the orig and ?h.sphere.dist0.jacobian.reg as the target for consistency On Fri, 21 Dec 2007, Michael Harms wrote: A followup on issue (2): If I'm understanding you correctly, the -jacobian_dist0 flag and associated

Re: [Freesurfer] jacobian analyses

A followup on issue (2): If I'm understanding you correctly, the -jacobian_dist0 flag and associated ?h.jacobian_dist0 file are supposed to get at the TOTAL distortion, starting at ?h.white, when you morph without any distance constraints. If that is the intent, then I'm confused about the synta

Re: [Freesurfer] jacobian analyses

Hi Mike, 1. This will include distortions in the spherical mapping as well as the spherical registration (note that global area scaling is taken out, unless you specify -n). I think this is probably what you want, since otherwise the spherical transformation could wash out interesting things

Re: [Freesurfer] Cluster thresholding

Hi, Just th9ought I would chime in here. I have the same understanding as Pratap as long as by "primary cluster forming threshold" you are referring to is the vertex wise p-value. The cluster wise p-value you choose after the simulation does not have to be derived from this value. But perhaps both

[Freesurfer] jacobian analyses

Hello, I'm going back and running the jacobian analyses (using v4 recon-all) so that I can look at distortion arising from the spherical registration. Couple questions about what is going on "under the hood": 1) When using the -jacobian_white flag, the command executed is: mris_jacobian ?h.white

Re: [Freesurfer] Cluster thresholding

Doug, please correct me if i am wrong and add if need to. > Hi, > After wrestling with this a bit, I think I get the idea (finally!). > Just to confirm: > > 1- set a primary threshold in the mri_glmfit command, e.g., --sim > perm 5000 1.3 will run 5000 permutations with the primary cluster > formi

Re: [Freesurfer] question about control points

p.s. the topology correction probably failed because there multiple breaks/defects along the white matter strand. Be sure to fill all of them that really should be white matter. On Fri, 21 Dec 2007, Matt Colvin wrote: Freesurfer Folks, I am having trouble with a handful of subjects in which t

Re: [Freesurfer] question about control points

Hi Matt, this is almost certainly a topology correction problem, not a control point one. You can see from your snapshots how the superior temporal gyrus is (incorrectly) disconnected from the body of the temporal lobe. This results in a topological defect, that is incorrectly fixed by the to

Re: [Freesurfer] ERROR: talairach_afd: Talairach Transform:

Hi Roberto, can you visually inspect the talairach transform using tkregister2 and see if it is correct? chers, Bruce On Fri, 21 Dec 2007, Roberto Roiz Ssantiáñez wrote: Dear all. I have tried to run “recon-all -s subject -autorecon1” with a sequence acquired in a 3T Philips scanner. I hav

[Freesurfer] ERROR: talairach_afd: Talairach Transform:

Dear all. I have tried to run “recon-all -s subject -autorecon1” with a sequence acquired in a 3T Philips scanner. I have transformed the image into Analise using MRIcro and then run recon-all. I got the following error: talairach_avi done # [EMAI