[Freesurfer] glmfit mismatch between X and C with same no of columns

2017-03-27 Thread Clara Kühn
Dear Freesurfer experts, I'm trying to run a repeated measures anova as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova I have 40 subjects with 2 time points each, so it's quite a large matrix. When running the mri_glmfit command I get the following error: ERROR

[Freesurfer] Fwd: -dura_thresh

2017-03-27 Thread Octavian Lie
Can anybody comment on the new dura_thresh flag? See below, Many thanks, Octavian. -- Forwarded message -- From: Octavian Lie Date: Sat, Mar 11, 2017 at 9:28 AM Subject: -dura_thresh To: "freesurfer@nmr.mgh.harvard.edu" Dear All, In FS6.0.0, this flag is added to manually ad

Re: [Freesurfer] Error in aparcstats2table

2017-03-27 Thread Douglas N Greve
That command line works for me. What version of FS are you using? Is that the only thing that gets printed to the terminal? On 03/26/2017 02:40 PM, shi yao wang wrote: > Dear FS experts: > I am using aparcstats2table command to generate mean thickness of > group subjects. > > my commands: > apa

Re: [Freesurfer] group analysis of large data sets

2017-03-27 Thread Douglas N Greve
I don't think there is a maximum size. You would do the big analysis the same way as the small. On 03/26/2017 07:54 PM, Wang, Xin wrote: > > Hello, FreeSurfer Group, > > What is the maximal matrix size for glm_fit process? > > How to use FreeSurfer for group analyses of more than 2000 subjects,

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

2017-03-27 Thread Douglas N Greve
Need command line and terminal output On 03/27/2017 09:08 AM, Clara Kühn wrote: > Dear Freesurfer experts, > > I'm trying to run a repeated measures anova as described here: > https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova > > I have 40 subjects with 2 time points each, so it's

[Freesurfer] Moving fa map from talairach to MNI

2017-03-27 Thread John Anderson
Hi Freesurfer experts, I followed "dt_recon" pipeline https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon to analyze DTI data. The analysis ran smoothly without any issues. I want to inquire waht is the correct method to move "fa-tal.nii" to MNI152_2mm Is this command correct"? mri_vol2vol --mov f

[Freesurfer] white matter disease

2017-03-27 Thread Rockers, Elijah D.
Hello, We have a large number of subjects processed with the default settings of recon-all. Unfortunately the presence of white matter creates problems when creating the white matter surface. There are large hypo-intensities in the white matter which badly distort the surfaces in multiple areas

[Freesurfer] display ROI mean values for FS atlas

2017-03-27 Thread X K
Hi, I am doing a project with the Desikan-Killiany atlas. After some ROI analysis, I've got some values for each area. Now I want to display these values in the brain 3D space. The values are Z statistic scores, so there are both positive and negtive values (I want Z=0 to be in the middle of the c

[Freesurfer] measuring basal ganglia volume

2017-03-27 Thread shi yao wang
Dear FS experts: We are measuring population based basal ganglia volume. Except the absolute volume of BS, any other parameters could be a reliable marker to reflect BS volume? such as ratio of total subcortical GM volume. Thanks! Lawrence ___ Freesurfer

Re: [Freesurfer] display ROI mean values for FS atlas

2017-03-27 Thread Bruce Fischl
so you want to color each parcellation unit with the same color on say the fsaverage surface? I think people have done that, so hopefully someone else has instructions for you cheers Bruce On Mon, 27 Mar 2017, X K wrote: Hi, I am doing a project with the Desikan-Killiany atlas. After some