Hi Bruce, I'm running Ubuntu version 14.04 LTS and Freesurfer version 1.379.2.65. I am only trying to run the Bert test lines when I come up with the segfault error I mentioned earlier so command line : tkmedit bert orig.mgz which comes up with ERROR: A segfault has occurred. This is not your fault, but is most likely an unrecoverable error and has made the program unstable. Please send the contents of the file .xdebug_tkmedit that should be in this directory to freesurfer@nmr.mgh.harvard.edu. which is the only message displayed at that point. Any suggestions? Nikita Zhitkevich
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 127, Issue 37 To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 24 Sep 2014 12:00:02 -0400
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Today's Topics:
- longitudinal analysis and linear mixed effects models (Emma Thompson)
- Re: Pial Surface Incorrect For Native T1 (Zachary Greenberg)
- Segfault Error (Nikita Zhitkevich)
- how to extract the individual cortical thickness or volume value of significant cluster after RFT correction (wang kangcheng)
- Re: how to extract the individual cortical thickness or volume value of significant cluster after RFT correction (wang kangcheng)
- Re: Segfault Error (Bruce Fischl)
- Re: longitudinal analysis and linear mixed effects models (Martin Reuter)
- Re: Vertex wise analysis and area/pial area/volume interpretation (Las Blawimo)
- Brainhack Eastern Standard Time - Boston October 18-19, 2014 (MCLAREN, Donald)
- watershed problem (Anastasia Klimovich-Smith)
- Re: how to extract the individual cortical thickness or volume value of significant cluster after RFT correction (Douglas N Greve)
- Re: Pial Surface Incorrect For Native T1 (Douglas N Greve)
- Re: Scatter plot from mri_glmfit analyses (Douglas N Greve)
- Re: possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences (Douglas N Greve)
- Re: Volume to surface coordinates (Douglas N Greve)
Message: 1 Date: Tue, 23 Sep 2014 17:55:27 -0400 From: Emma Thompson voneconomos@gmail.com Subject: [Freesurfer] longitudinal analysis and linear mixed effects models To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CA+BXJQJHWhSi2p+Yr25Cb_yUxcb-hEwPwCbdtV96Y=ub+Qh_8A@mail.gmail.com Content-Type: text/plain; charset="utf-8"
Hi FS, I want to conduct a within-subjects longitudinal analysis, I thought I would be able to run a LME model in QDEC but this doesn't seem to be the case at all, is this correct? It seems I have to do everything using Matlab (big sigh).
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
I have already preprocessed the data: 1) cross for all time points, 2) base, and then 3) long according to the awesome tutorial provided by FS.
I have only one group, a patient population that was scanned prior to (bseline) and at various time points (3 time points post) following treatment. Would you agree that the best analytical approach for me would be the LME model, especially since I have a few subjects with a couple of missing post-treatment time points?
Is there any way you would recommend another approach using QDEC?
Lastly, I have done everything in FS version 5.1, I'm considering upgrading to 5.3, since my freeview software seems to be out of date. It also seems that the Matlab tools I need to run LME are only available in FS version 5.2. At this point a little concerned since I'm hoping I didn't waste a bunch of time just realizing all this now, would upgrading to 5.3 negatively impact all the work I've done thus far using version 5.1?
Thanks for the help!!