[Freesurfer] Announcing Release of PySurfer 0.3

2012-04-26 Thread Michael Waskom
Dear All, We are pleased to announce the 0.3 release of PySurfer, a Python-based package for visualizing Freesurfer data. This release includes bugfixes and quite a few enhancements, including: - Tools for reading and manipulating MEG data from MNE (thanks to work from Martin Luessi and Alex Gram

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29

2012-04-26 Thread Bruce Fischl
glad it works, although it's a bit of a mystery why it was broken. cheers Bruce On Thu, 26 Apr 2012, Andrew C Yourich wrote: > I've replaced my old mris_expand file with the one downloaded from the link > below, and now it is working perfectly. Thank you so much to all of you who > helped me r

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29

2012-04-26 Thread Andrew C Yourich
I've replaced my old mris_expand file with the one downloaded from the link below, and now it is working perfectly. Thank you so much to all of you who helped me resolve this issue. I really appreciate it. - Andrew From: Nick Schmansky [ni...@nmr.mgh.harv

[Freesurfer] using "label" flag w tksurfer

2012-04-26 Thread Justin Baker
I've ported a tksurfer call from one system (NCF, where it was working) to another (MGH) and now the "label" argument is no longer recognized. Here is the command: tksurfer fsaverage5 lh inflated -o test.nii.gz -fthresh 3 -fmid 4.301 -fslope 1 -colscalebarflag 1 -label lh.17Networks_LH_ContA_Cing

[Freesurfer] 5.1.0 volume analysis in native space

2012-04-26 Thread Maya Rosen
Hi all, In v5.1.0 is there a way to do a volume analysis in native space? I know when you do mkanalysis for the surface you can use -surface self. But for the volume analysis the only flag I see is -mni305. Is there some way to give it a native space flag for the volume? Thanks! Maya __

Re: [Freesurfer] your insight: parameter definition and --tnullmin necessary?

2012-04-26 Thread Douglas N Greve
On 04/26/2012 09:19 AM, Betina Ip wrote: > Dear Doug, > > Thanks for your reply. I will compare conditions against the NULL, but > the ultimate aim is to compare conditions against each other. The > effect I am looking for will be very small, so I am trying to make > sure I optimise the design

Re: [Freesurfer] About GroupAnalysis

2012-04-26 Thread Douglas N Greve
Hi Bobo, if you run mri_glmfit with --help, it will give you lots of information about how it works. doug On 04/25/2012 09:54 PM, bowan...@mail.ustc.edu.cn wrote: > Dear All, > I am learning GroupAnalysis and I have some problem about the vector that > embodies the hypothesis we want to test

Re: [Freesurfer] your insight: parameter definition and --tnullmin necessary?

2012-04-26 Thread Betina Ip
Dear Doug, Thanks for your reply. I will compare conditions against the NULL, but the ultimate aim is to compare conditions against each other. The effect I am looking for will be very small, so I am trying to make sure I optimise the design- I really appreciate your insight. Miezin et al., 20