Re: [Freesurfer] LME univariate data

Dear Kersten, Thanks, I find it. And I have other questions: 1. The intercepts all set as one, so in this model it doesn't separate different subjects, or can say no individual subject change rate? 2. Should we set age according to different timepoint, or just use baseline age? Thanks, Lanbo On

Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix

Stop sending me this shit > Wiadomość napisana przez Kai Ohmstedt w dniu > 13.03.2018, o godz. 02:02: > > Hi Douglas, > > thank you for the explanation of the contrasts, this helped a lot! > > > All the best, > > Kai > > 2018-03-12 18:20 GMT+01:00 Douglas N.

Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0

Looks good to me! Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: Tuesday, March 13, 2018

[Freesurfer] Longitudinal strean including more than an image per time point

Dear all, We want to run the longitudinal FS processing pipeline for our study, which has 4 time points. The 1st one was acquired with a radiofrequency head coil of 8 channels. Then, due to unexpected problems, some subjects at the 2nd time point were acquired with a different head coil of 16

[Freesurfer] LME univariate data

Dear Experts, Hi, There is no example detail on website of LME tutorial. I have some question about it. Could you send me the table of ADNI univariate example data? Thanks, Lanbo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer6.0 failure

Hi Naka we have tracked down this problem and should have a patch soon cheers Bruce On Tue, 13 Mar 2018, Naka Beguedou wrote: > > > Hello, > I allow myself to send you this mail in order to have some informations. we > have a problem concerning the segmentation of FREESURFER6.0 > Indeed for

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

glad it worked out Bruce On Tue, 13 Mar 2018, Chris Adamson wrote: So I think I have fixed it. When I swapped the volume used for geometry to radiological from neurological everything worked. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] make_average_subject monkey data

Dear Experts, I'm trying to average two monkey brains. I run this command line: make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkeys but it ended with errors. I run the recon-all for both monkyes with the option -notal-check because I had problems with the Talairach

Re: [Freesurfer] LME univariate data

Hello, On Di, 2018-03-13 at 21:48 +0100, lanbo Wang wrote: > Dear Kersten, > > Thanks, I find it. And I have other questions: > 1. The intercepts all set as one, so in this model it doesn't > separate different subjects, or can say no individual subject change > rate? If I understood correctly,

[Freesurfer] dt_recon error: MatrixReadTxT: could not scan value [1][1]

Hello FreeSurfer Developers, I am trying to follow the diffusion processing pipeline describe in this tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIDataAnalysisProcessingStream However, I keep getting an error when using dt_recon. For background, my input is

Re: [Freesurfer] FSdev compilation error

Hi Victor, thanks, can you send the config.log for the original issue where configure fails and “--with-mni-dir=“ isn’t specified. best, Andrew On March 12, 2018 at 10:07:33 AM, Victor Hansen (victor.han...@nru.dk) wrote: Hello Andrew Attached is our config.log

Re: [Freesurfer] LME univariate data

Hello Lanbo, the univariate example data can actually be downloaded from the LME tutorial website: Search for: "An optional sample dataset which can be used to become familiar with the LME Matlab tools can be found here". The linked tar.gz archive contains two folders, one for the univariate and

Re: [Freesurfer] Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?

Any updates or ideas in extracting histogram data from mri_segstats? On Sun, Mar 11, 2018 at 1:16 PM Yash Patel wrote: > Dear all, > > I am using mri_segstats to obtain intensity values from each of the 34 > cortical parcellations in the Desikan-Killiany Atlas;