Re: [Freesurfer] LME toolbox - univariate

Thank you Martin! For only one group, would the design matrix be the same but intercept=Group=all ones? Yij = ß1 + ß2*tij +ß3*Group + ß4*Group *tij + ß5*Genderi + ß6*Agei + ß7*ICVi+ b 1i + b2i*tij + eij Regards, Yolanda 2013/5/28 Martin Reuter mreu...@nmr.mgh.harvard.edu Hi Yolanda, since

[Freesurfer] Post-Doctoral position in brain imaging and computational morphometry – University of Geneva

Applications are invited for a funded Post-Doctoral position in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include

Re: [Freesurfer] LME toolbox - univariate

For only one group you don't need a group variable. you'd drop beta 3 and 4 terms. Yolanda Vives yvi...@pic.es wrote: Thank you Martin! For only one group, would the design matrix be the same but intercept=Group=all ones? Yij = ß1 + ß2*tij +ß3*Group + ß4*Group *tij + ß5*Genderi + ß6*Agei +

Re: [Freesurfer] Representation of average curvature on subject's curvature

Hi Sophie I'm not sure there's an easy way as those weren't made entirely within freesurfer. I guess you could create a label of all positive curvature and use the outline mode to show multiple labels Bruce On Wed, 29 May 2013, Sophie Maingault wrote: Hi FreeSufer Experts,  I would

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

I mean; if you devide the number of vertices by the area per aparc-parcellation, some parcellations have relatively more vertices per mm^2 as others. If you now would compute the average thickness in for example the lobe-parcellation, the thicknesses of some areas (the parcellations with

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

I think it depends on how you do the computation. You would probably weight each vertex by the area then sum then divide by the total area and this is probably not much different than just averaging over vertices without taking the area into account. doug On 5/29/13 9:16 AM, Martijn

Re: [Freesurfer] SUMA and FSFAST

sorry, I've never used SUMA. Maybe Ziad can chime in (though he's probably never used FSFAST!) doug On 5/28/13 8:57 PM, Joseph Dien wrote: I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to

Re: [Freesurfer] head motion values

fmcpr.mcdat are the motion estimates (mm and degrees). mcprextreg is the motion correction parameters after analysis using a PCA, which is why there is such a huge difference. By default we use the top 4 components. doug On 5/28/13 8:28 PM, Joseph Dien wrote: I have a follow-up question for

[Freesurfer] Contrast of three groups

Hi FreeSurfers, I have a more statistical question: I have three groups of subjects and I want to examine the effect of a continuous variable (cognition). Is it possible to examine three groups? Or should I do pairwise comparisons? What would the contrast than look like? Something like this:

Re: [Freesurfer] Contrast of three groups

Hi Doug, Thanks for the answer. How can I examine differences between the groups? Best Heidi Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: woensdag 29

Re: [Freesurfer] beta weights from FS-Fast analysis

Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional

Re: [Freesurfer] Contrast of three groups

If you want to look for an interaction between your cog score and group, then use the following contrast: 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 1 0 -1 This is an F-contrast with two rows doug On 05/29/2013 11:33 AM, Jacobs H (NP) wrote: Hi Doug, Thanks for the answer. How can I examine differences

Re: [Freesurfer] SUMA and FSFAST

Thanks Ziad, looks like it is similar to FSFAST. doug On 05/29/2013 11:50 AM, Ziad Saad wrote: Hi Joe, As Doug guessed, I never used FSFAST so I can't really tell you much about how they differ. SUMA will require you use FreeSurfer to create the surfaces and warp them to standard

[Freesurfer] Reposition Surface

Just a question about the Tools -- Reposition Surface... feature in Freeview. Is that up and running? Is there any accompanying documentation? Thanks. -Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Defacing with mri_deface

The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files /usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca The former exists where it should, the latter does not exist at that

[Freesurfer] R: Re: very slow analysis with recon-all

Bruce and Sebastian thank you very much. I have checked the files but they are all wrong. These are the image info: data_type FLOAT32dim1 280dim2 240dim3 240dim4 1datatype 16pixdim10.584741pixdim2 1.041269pixdim3

[Freesurfer] R: R: Re: very slow analysis with recon-all

I apologize. This is the correct info:data_type INT16dim1 280dim2 240dim3 240dim4 1datatype 4pixdim1 0.584741pixdim21.041269pixdim31.041269pixdim4 0.00cal_max0.cal_min

Re: [Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields

I usually use this little bash script (named myrecon) to process my images. #!/bin/bash mkdir ~/freesurfer/subjects/$1/mri/orig -p cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/ recon-all -all -s $1 -cw256 -hippo-subfields -qcache With this script I get the entire -all

Re: [Freesurfer] Defacing with mri_deface

Hi Steve I think recon-all -deface only creates the orig_defaced.mgz which you can then use with mri_mask to remove facial features from whatever volumes you want. I don't have write permissions to that directory, but I'll see if I can get help to copy it. cheers Bruce On Wed, 29 May 2013,

Re: [Freesurfer] mris_divide_parcellation color table error

Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that

Re: [Freesurfer] mris_divide_parcellation color table error

Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon

Re: [Freesurfer] mris_divide_parcellation color table error

hmmm, I haven't run that code in a long time. Are the colors different but not visually so? That is, do the rgb values differ by 1 or 2 or something like that? Or are they actualy identical? On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May

Re: [Freesurfer] beta weights from FS-Fast analysis

On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz