Re: [Freesurfer] Fwd: comparing lme models

Hi Jorge, My original model is: Intercept + centered age + group + centered age x group + sex; and since I have only two time points I can have only one random factor (as you've stated previously). I have used intercept as the random factor. So, based on your reply, I should fit this model for

Re: [Freesurfer] doubt regarding wm.mgz non wm voxels

Hi Elisa if the surfaces are correct (and they seem to have done an impressively good job) then you don't need to. While it worked for this case, I would be a bit concerned that the surfaces won't recover from wm.mgz inaccuracies in others ones though. You might try setting wlo to above the

Re: [Freesurfer] doubt regarding wm.mgz non wm voxels

Thank you. Best, elisa Il 18/dic/2014 16:10 Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Elisa if the surfaces are correct (and they seem to have done an impressively good job) then you don't need to. While it worked for this case, I would be a bit concerned that the surfaces

Re: [Freesurfer] doubt regarding wm.mgz non wm voxels

Just one additional issue: what am I supposed to do if (please see attached pictures) the wm.mgz file correctly does not include gray matter voxels, but the yellow surface goes into the gray matter? How can I fix this error? Thank you. Best, elisa [image: Immagine in linea 1] [image: Immagine

Re: [Freesurfer] longitudinal statistics LGI

HI Jorge, Thanks for your quick reply. What should we use for the contrast matrix? the freesurfer LME wiki has: CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];​ But I wasn't sure if that applies to our analyses. please excuse the naive questions, we are new to

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

OK, I've figured out what's going on. The cluster @ threshold of 1.3 in superior temporal breaks up into 3 very small clusters when the threshold is changed to 2.0, none of which are significant. There is a cluster in middle temporal at 1.3 but it is not very significant (p=.17), but it

Re: [Freesurfer] retinotopy in subject volumetric space

What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to

Re: [Freesurfer] retinotopy in subject volumetric space

I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote:

[Freesurfer] surface template N

We are planning to generate a surface template from edited reconstructions of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum number of subjects should be used to generate the template? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of

Re: [Freesurfer] surface template N

Hi Jason, I saw this last week. I *think* the original template was on 40 brains, so 40 seems like a good number. In my opinion the bigger issue is the 8 year age range. A 3-year-old's head is much smaller than an 11-year-old's. I'm not sure I would mix them, and if there are enough subjects

Re: [Freesurfer] From bedpostX and recon-all to tracula

You may have to transpose the bvecs and bvals files. I think that's how Tracula expects them. You can use the attached script to do it. On 12/17/2014 09:18 PM, Katherine Damme wrote: Thanks! That was exactly it! It was a FAT server and so that resolved that issue. Tracula is claiming that

[Freesurfer] Clarification regarding group specific average template creation

Hello, My question is regarding the registration procedure using a group specific average template. I ran recon-all for my group(with 100 subjects), created an average subject using make_average_subject and then used recon-all qcache by referencing the average template that I just created. I

Re: [Freesurfer] longitudinal statistics LGI

Hi Jorge, One more newbie question. what's a good way to visualize the lhstats1.lreml values across the vertices? Thanks Jon From: jorge luis jbernal0...@yahoo.es Sent: Wednesday, December 17, 2014 9:25 AM To: Freesurfer support list; Jon Alan Wieser Cc:

Re: [Freesurfer] doubt regarding wm.mgz non wm voxels

Hi Elisa try the -seg-wlo I sent you before. Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Just one additional issue: what am I supposed to do if (please see attached pictures) the wm.mgz file correctly does not include gray matter voxels, but the yellow surface goes into the gray matter?

Re: [Freesurfer] surface template N

Hi Jason I would say at least 15, but you can also just check to see when things start to asymptote. I think Christophe found there were diminishing returns after 12 or so, but things have changed somewhat since then, and of course it will depend on the variance on your population. cheers

Re: [Freesurfer] using mri_convert with multiframe dicom

Hi Doug, Lauren has just reuploaded the multiframe phantoms to your dropbox. Thanks so much for taking a look at this. Jenny Gurney CNDA/Wash U The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the

Re: [Freesurfer] Clarification regarding group specific average template creation

Hi Prad no, everything is still ni fsaverage space. You would need to run mris_make_template to create a new template, then rerun mris_register cheers Bruce On Thu, 18 Dec 2014, Bharadwaj, Pradyumna - (prad) wrote: Hello, My question is regarding the registration procedure using a

Re: [Freesurfer] Tracula output variability reinit

Hi Peggy - The reinit option is meant to use when you don't have a valid-appearing tract the first time (you have a tract that looks like a single line, which means that the first initialization of the path was poor, i.e., outside the white matter or something like that). If you have a

Re: [Freesurfer] Tracula Question

Hi Emily - One should be a symbolic link to the other, so they should be the exact same file. a.y On Tue, 16 Dec 2014, Emily Louise Belleau wrote: __

Re: [Freesurfer] From bedpostX and recon-all to tracula

Hi Kate - The option to use row-formatted (instead of column-formatted) gradient tables was added in a tracula update that came out after freesurfer 5.3 was released. If you want to use this format, you can download the update here:

Re: [Freesurfer] TRACULA pathway recon failure

Hi Emad - By default, tracula will use aparc+aseg_mask and NOT lowb_brain_mask. So you should make sure aparc+aseg_mask contains the right amount of brain, and then rerun the steps of trac-all that come after the -mask step. a.y On Tue, 16 Dec 2014, Emad Ahmadi wrote: Hi Anastasia, I’ve

[Freesurfer] Tracula: missing or incomplete tracts

Hi - I'm having difficulty with missing or incomplete tracts most of my subjects. I'm hoping for suggestions on where I can look for data problems. The majority of my subjects have at least one missing/incomplete tract, but the specific problematic tract varies across subjects (e.g., one subject

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

Hi Doug, Thanks, that makes it very clear. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265