Re: [Freesurfer] visualize subcortical areas in tksurfer?

Hi Daniel I wouldn't advise this - you will miss most of the activation unless it happens to be right next to where the surface runs adjacent to the structure of interest. For subcortical structures you are better off showing the results in slices. cheers Bruce On Mon, 23 Feb 2015, Yang,

[Freesurfer] Using -qcache command multiple times

Hello, I had a question about using the -qcache command for smoothing. Previously, the -qcache command was used on several subjects in my dataset, and since then, these subjects have undergone some manual edits (control points, edits to wm.mgz, etc.). Currently, I’d like to run the -qcache

[Freesurfer] Older version (5.0) on newer OSes

Hello everyone, I have a quick question about the feasibility of running FreeSurfer v5.0 on either RedHat/Centos 6.x or a newer Debian install. We want to run some new subjects but compare them to subjects run 5 yrs ago with FreeSurfer 5.0. Running all of the old subjects again in v5.3 is

Re: [Freesurfer] treatment effect compare to controls

Hi, yes, the first is to stack all the data into a single file (on your study average, usually that is fsaverage). The second steps smoothes the data. You can use different smoothing levels, depending on your data. Usually 10 or 15 is a good number. The data will automatically be taken from

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows:  mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166

[Freesurfer] mri_glmfit-sim Error

Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows:  mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166

Re: [Freesurfer] treatment effect compare to controls

Hi and thanks Martin for your help, I am trying to do mixed effect analysis, should I use the registered to template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1) and how should the aded.table.dat look like? Do I need to run : mris_preproc --qdec-long qdec.table.dat --target

Re: [Freesurfer] RAM Replace

I would very much hope that replacing the RAM wouldn't change anything Bruce On Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote: Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely

Re: [Freesurfer] RAM Replace

Thanks, Bruce. I am asking this because I believe that changing the processor or the operational system could change the processing. If I got it correctly, it is expected that it is not the same for the RAM. Am I correct? Thanks again, Pedro. On Feb 23, 2015, at 21:50, Bruce Fischl

Re: [Freesurfer] RAM Replace

yes, it would be pretty strange if swapping out ram changed the results On Mon, 23 Feb 2015, Pedro Rosa wrote: Thanks, Bruce. I am asking this because I believe that changing the processor or the operational system could change the processing. If I got it correctly, it is expected that it

[Freesurfer] RAM Replace

Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely processed, but there are a few subjects whose acquisition are yet to be done. I would like know whether I could process such