[Freesurfer] Comparison of the slope of the pvr analysis between groups

Dear FS experts, There is already a post about that but the concerned person never answered so there is no solution. I’m currently running per-vertex analyses with the --pvr flag of mri_glmfit command. I did correlations between 2 vertex-wise variables correcting for age. I also would like to

[Freesurfer] Qdec stats question

Hi Freesurfer Experts, I have used freesurfer smoothed images (lh.thickness.fsaverage.fwhm15.gii) to perform a cortical thickness analysis. I used qdec with a surface-based morphometric analysis to compare two groups. As my discrete fixed factor I used group membership. As Nuisance factors I used

Re: [Freesurfer] white matter edits not incorporated

Hi, I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface. I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8 for those at Martinos the new

Re: [Freesurfer] white matter edits not incorporated

That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”). I think some of the subsequent back-and-forth with Bruce and Nick was off the list, so I’ve included the key email (where Bruce diagnosed the problem) below. Has this been fixed in the f

Re: [Freesurfer] Hippocampal subfields, stuck?

Dear Maximilià, first of all, sorry for the late response. We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it exists. If this is not the case in your system, maybe you could create an alias from 'mv' -> 'mv -f' before calling recon-all? Cheers, /Eugenio Juan Eugenio Ig

Re: [Freesurfer] white matter edits not incorporated

Hi Daniel I'm out if town , can you remind me next week? This is fixed in v6 I think if you want to just run the pial stuff in it Bruce > On Apr 21, 2016, at 10:41 AM, dgw wrote: > > Hi, > > I followed the advice, and the White Matter surface looks much better; > however, now the pial surfac

[Freesurfer] Qdec interface issue

Hello, I am working on measuring cortical thickness of a patient group. I am using Ubuntu 14.04 Somehow, if I use command line to perform the analysis, Freesurfer/qdec is working fine but if I use Qdec interface, it works fine initially but when I switch to display window, it doesn't allow me to

Re: [Freesurfer] lme model for within-subjects repeated measures design

Hi Martina, so you don't have a baseline (no treatment) measurement? If you have a treatment at T0, you mean during an interval before T0, right? But since you did not scan before that treatment, you cannot quantify that change? The design is not clear to me. About the random effect (with on

Re: [Freesurfer] mixed models and longitudinal streaming

Hi Angela, to get the fs_write_Y to work, you would first need to set mri.volsz(4) = 1 (to tell it to write only a single frame). But for writing significance maps, you can use fs_write_fstats (as you did). Usually you don't describe the data, but simply capture the overlay of the p values on

Re: [Freesurfer] white matter edits not incorporated

Hi Mike yes, I think it is fixed. Daniel: can you try out dev and see if it fixes this for you? Bruce On Thu, 21 Apr 2016, Harms, Michael wrote: That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”). I think some of the subsequent ba

Re: [Freesurfer] white matter edits not incorporated

Hi, I solved it (with help from a colleague) by just calling the individual mri_make_surfaces command separately (adjusting the nowhite), and the subsequent ones through the flair pial command. I am now running -make all, to finish the rest (note it did miss one step in the re-start: it didn't re-

Re: [Freesurfer] white matter edits not incorporated

yes, I think that's what V6 does I think On Thu, 21 Apr 2016, dgw wrote: Hi, I solved it (with help from a colleague) by just calling the individual mri_make_surfaces command separately (adjusting the nowhite), and the subsequent ones through the flair pial command. I am now running -make all,

Re: [Freesurfer] lme model for within-subjects repeated measures design

Hi Martin Thank you very much for your response! To clarify the design: There are 44 subjects, all have been scanned twice and thus have repeated measures of cortical thickness. 22 subjects were first (T0) scanned 2 hours after a placebo treatment. Some days later, the identical subjects were

Re: [Freesurfer] lme model for within-subjects repeated measures design

Thanks, what I mean is in order to quantify a treatment effect for the subjects that received treatment at T0, you would need another scan before that (Tminus1). You would need three time points: group1: baseline, placebo, treatment group2: baseline, treatment, placebo you could then test if

Re: [Freesurfer] mixed models and longitudinal streaming

thank you! Martin Reuter ha scritto: > Hi Angela, > > to get the fs_write_Y to work, you would first need to set > mri.volsz(4) = 1 > (to tell it to write only a single frame). > > But for writing significance maps, you can use fs_write_fstats (as you did). > > Usually you don't describe the d