[Freesurfer] glm question

Dear FreeSurfer experts, I'm doing some group analyses and I'm a little stocked with this: I have Six Groups (2 Factors, one with three levels and the other one with two levels), and one covariate. I don't know the rule for setting the contrasts for an ANOVA and for the interaction between t

[Freesurfer] CUDA comparable to non-CUDA?

Hi FreeSurfer Experts, Just a quick question: Generally speaking, assuming everything else remains the same, are subjects run through a CUDA-enabled recon-all comparable to subjects run through recon-all without CUDA? Thanks, Marcus Marcus N Schmidt Department of Child & Adolescent Psychiatry

Re: [Freesurfer] CUDA comparable to non-CUDA?

We assume that. On Tue, Mar 8, 2011 at 09:58, Marcus N Schmidt wrote: > Hi FreeSurfer Experts, > > Just a quick question: Generally speaking, assuming everything else remains > the same, are subjects run through a CUDA-enabled recon-all comparable to > subjects run through recon-all without CUDA

Re: [Freesurfer] CUDA comparable to non-CUDA?

On Tue, 2011-03-08 at 13:58 +0100, Marcus N Schmidt wrote: > Just a quick question: Generally speaking, assuming everything else > remains the same, are subjects run through a CUDA-enabled recon-all > comparable to subjects run through recon-all without CUDA? There are differences, which are ine

Re: [Freesurfer] CUDA comparable to non-CUDA?

Thanks for the info. Richard, it would be great to hear what you find. -marcus Marcus N Schmidt Department of Child & Adolescent Psychiatry Erasmus MC Rotterdam, The Netherlands On Mar 8, 2011, at 3:17 PM, Richard G. Edgar wrote: > > On Tue, 2011-03-08 at 13:58 +0100, Marcus N Schmidt wrote:

Re: [Freesurfer] Intensity Problem

Thanks Bruce, The parcellation looks good in general, except that this part of the temporal lobe is consistently missed due to that anomaly. Best, Matt On Fri, Mar 4, 2011 at 7:52 AM, Bruce Fischl wrote: > Hi matt > Does the parcellation look correct? If so you might be ok if you stay away > fr

[Freesurfer] Pial view

Hi Everyone, I am hoping to visualize the insula using the pial view in TkSurfer. Is there a way to make the surfaces translucent, or to crop away specific areas? I would like to use the pial view instead of inflated views to do this. Thanks, Allie Rosen, MSc Graduate Student, Department of Neur

Re: [Freesurfer] Intensity Problem

then maybe you are ok On Tue, 8 Mar 2011, Matt Russell wrote: > Thanks Bruce, > > The parcellation looks good in general, except that this part of the > temporal lobe is consistently missed > due to that anomaly. > > Best, > Matt > > On Fri, Mar 4, 2011 at 7:52 AM, Bruce Fischl > wrote: > >> Hi m

Re: [Freesurfer] Pial view

I think you can do this in freeview cheers Bruce On Tue, 8 Mar 2011, Allie Rosen wrote: > Hi Everyone, > > I am hoping to visualize the insula using the pial view in TkSurfer. Is > there a way to make the surfaces translucent, or to crop away specific > areas? I would like to use the pial view in

Re: [Freesurfer] qdec problems

Wang, have a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis and also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons which itself has some links explaining the necessity for correcting for multiple comparisons. the newer qdec has the

[Freesurfer] Cortical thickness in the template space

Hello, We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone p

Re: [Freesurfer] Cortical thickness in the template space

Aize, run: recon-all -s subjid -qcache -measure thickness and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space. n. On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote: > > Hello, > > We try to look at the two

[Freesurfer] Newbie - problems compiling project tree

Hi All, I am having some problems compiling freesurfer . I checked out the recent development version from the CVS, ran "setup_configure" successfully, but upon "./configure", I end up with the following annoying message: checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib

Re: [Freesurfer] Newbie - problems compiling project tree

libnetcdf-dev or netcdf-dev will do the trick On Tue, Mar 8, 2011 at 19:42, Shay Ohayon wrote: > Hi All, > > I am having some problems compiling freesurfer . > I checked out the recent development version from the CVS, ran > "setup_configure" successfully, but upon "./configure", I end up with

Re: [Freesurfer] Newbie - problems compiling project tree

Hi All, OK. Installed those packages, but now I end up with this error: checking for miopen in -lminc... no configure: error: FATAL: minc lib not found. Set LDFLAGS or --with-mni-dir. I installed libminc2-1, libminc-dev and minc-tools, but I still get this error. How do I proceed ? Thanks! -

[Freesurfer] Aparc Cutting?

Hi Everyone, I'm wondering if it is possible to use the "cut" function in TkSurfer to delete specific atlas annotations. For example, can I create a label of my specific area of interest, inverse the label to highlight the rest of the brain, and then either cut out these regions or make them trans

Re: [Freesurfer] Aparc Cutting?

I've never used that, but you can use mris_annotation2label to break the annotation in to individual labels,then use mris_label2annot to put the ones you want back together. doug On 3/8/11 10:13 PM, Allie Rosen wrote: Hi Everyone, I'm wondering if it is possible to use the "cut" function in

[Freesurfer] Miao Wen wants to stay in touch on LinkedIn

LinkedIn Miao Wen souhaite se connecter à vous sur LinkedIn : -- Freesurfer, I'd like to add you to my professional network on LinkedIn. - Miao Wen Accepter l'invitation de Miao Wen http://www.linkedin.com/e/-qq80um-gl1us5y3-j/qaAr-Z_86TRZ5lXG