[Freesurfer] cluster size and FWER rough equivalence?

External Email - Use Caution We are working on a manuscript revision for an fMRI project that was analyzed with FS-FAST 5.3 years ago. We used mri_glmfit, and then we ran mri_surfcluster (instead of mri_glmfit-sim) with a vertex-wise threshold of p<0.001 and a cluster threshold of

[Freesurfer] Freeview surface annotation outline line thickness

External Email - Use Caution The freeview flag "annot_outline=1" is great for viewing results for significant clusters from mri_glmfit-sim. Is there a way to make the outlines thicker? With the default thickness, the outlines are difficult to make out in a multipanel figure. (The

[Freesurfer] bbregister and FLAIR

005/surf/lh.pial:edgecolor=red           \SLOTS005/surf/rh.pial:edgecolor=red           \SLOTS005/surf/lh.woFLAIR.pial:edgecolor=green \SLOTS005/surf/rh.woFLAIR.pial:edgecolor=green \-ras -37 -46 -42 Kayle Sawyer, PhD Athinoula A. Martinos Center for Biomedical ImagingMGH East Campus, Charlestow

Re: [Freesurfer] gammavar.mgh?

, Douglas N Greve wrote: > > Yes, that should work. > doug > > On 10/30/2013 03:35 PM, Kayle Sawyer wrote: >> Hi all, >> >> I would like to calculate the 95% confidence interval of the slope for a >> thickness cluster (vs age in years) produced by mri_glmfit

Re: [Freesurfer] sim ocn clusters mean effect size

Hi all, I would like to calculate the 95% confidence interval of the slope for a thickness cluster (vs age in years) produced by mri_glmfit-sim. I have obtained values for my clusters from gamma.mgh and gammavar.mgh using these two commands: mri_segstats --i gamma.mgh --seg m

[Freesurfer] sim ocn clusters mean effect size

Hi, Using FS 5.3, I ran a group analysis with mri_glmfit-sim to identify clusters where my two groups differed (along with many other analyses, e.g. age slope for each group). For each cluster, I would like to see what the mean group difference is, in mm. So, I used this command: mri_segstats

Re: [Freesurfer] Global thickness calculation

If you want the global thickness for all your subjects in a single table, use asegstats2table, e.g. aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile rh.aparc_stats.txt The first column will be the rh thickness, which you can average with the lh in a s

Re: [Freesurfer] Working with MEMPRAGE

Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize