Re: [Freesurfer] mri_cvs_register : output

Hi Elijah, Yes, it is. Lilla On Sun, 20 Mar 2016, Elijah Mak wrote: Hi Freesurfer Community, I am running mri_cvs_register for the spatial normalization and it seems to work very nicely on my set of DTI data in subjects with substantial atrophy.  However, I can't seem to find the file  co

Re: [Freesurfer] mixed models and longitudinal streaming

Hi Angela, the smooth function seems to be part of the curve fitting toolbox http://www.mathworks.com/help/curvefit/smooth.html so either that is missing, or your version is too old. You can skip the lowess Plot (it is just for initially checking the data). Make sure your M has the same number o

[Freesurfer] longitudinal data analysis

Hi Dr Martin I want to study the change in cortical thickness overtime in one group of subjects. I have only one group of subjects who scanned multiple times ( two time points and more) I followed the pipeline exactly as in wiki. I want to inquire about  X in this case . Is it supposed to be 1

Re: [Freesurfer] longitudinal data analysis

Hi John, X is the design matrix. The rows are the total number of time points for all subjects, the columns the different parameters of your model. In the wiki example, the first column is all 1s (intercept) the second is the time_from_baseline and other parameters that are in the matrix M

[Freesurfer] mris_fix_topology with ROI surface

Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface. The mri_sphere had a big chunk that was deleted and so I wanted to run mri

Re: [Freesurfer] longitudinal data analysis

Dear Dr Martin, Thanks you very much for your awesome clarification and your kindness!! Bests, John    Hi John, X is the design matrix. The rows are the total number of time points for all subjects, the columns the different parameters of your model. In the wiki example, the first column is

[Freesurfer] extracting pial surface area numbers...

Dear FS team, My question is how I should extract the measure of pial surface area from a significant cluster after group-analysis. I performed statistical analysis in QDEC, choosing pial surface area as the measure. I found a significant cluster. Now I would to extract the surface area of this c

Re: [Freesurfer] mris_fix_topology with ROI surface

Hi Ajay Florent Segonne developed some volumetric topology correction algorithms as well as surface-based ones when he was here. Try mri_topologycorrection and see how it works for you (although be warned that we haven't tried it in ages) cheers Bruce On Mon, 21 Mar 2016, Ajay Kurani wrot

[Freesurfer] Create a surface overlay with statistic results using AAL ROI

Hi all,   I have some statistical results for AAL 90 coordinates (correlation coefficients from network measurements x clinical data).   I would like to create an overlay to visualize in FreeSurfer standard (fsaverage) space, showing the areas with positive and negative correlations (and the scale

[Freesurfer] Postdoctoral Position in Infant Brain MRI Analysis

Postdoctoral research associate positions are available at the Infant Brain Mapping Lab in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill. Our current focuses are to better understand the dynamic and critical early brain

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

Hi Richard, The first part was smooth. I got it done pretty quickly (installing CUDA and setting it up!). However for the freesurfer portion I have two questions, 1. Bruce mentioned in another email thread that v6 beta should be out in a week or so after testing is completed. Should I wait for th

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

On 21 March 2016 at 19:59, Francis Tyson Thomas wrote: > The first part was smooth. I got it done pretty quickly (installing CUDA and > setting it up!). However for the freesurfer portion I have two questions, > > 1. Bruce mentioned in another email thread that v6 beta should be out in a > week o

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Hi Doug, Could you please upload epidewarp.fsl for FSL 5.x once again. Thanks! -Prad From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Tuesday, March 1, 2016 12:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Frees

[Freesurfer] Regarding: Freesurfer 6.0 dev version

Dear freesurfer experts, I am trying to do hippocampal subfields segmentation on Mac. I will greatly appreciate if freesurfer 6.0 version link is forwarded to me. With thanks and regards, Sampada Pre-doctoral student KGMU, Lucknow India ___ Freesurfer