[Freesurfer] Standalone Freeview?

econ tools, and if I install the latest FS, I will have to rerun the preprocessing... So is it possible to install the latest Freeview separately? Thanks. Jeni Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] Subcortical segmentation for PAG

Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni __

[Freesurfer] unit in 'search area' in the glmfit log

Hello, When running the Clusterwise Correction for Multiple Comparisons, I used a label as a mask to restrict search area. I want to find out the size of that label, so I guess I can pull that information out from the "mri_glmfit.log", specifically under 'searchspace'? Also I only see a numeric

Re: [Freesurfer] unit in 'search area' in the glmfit log

use > mri_segstats something like >> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh >> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat >> >> doug >> >> On 10/29/15 5:10 PM, Jeni Chen wrote: >> > Hello, >> > >

[Freesurfer] cwpvalthresh not specified

Hello, Just a quick question, if the 'cwpvalthresh' flag wasn't specified when running mri_glmfit-sim, the script will use the default .05 value, correct? Thanks for clairfying. Jeni Chen ___ Freesurfer mailing

Re: [Freesurfer] cwpvalthresh not specified

Phew! Thanks! jeni ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e

[Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

Hello,I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the entire simulation again. I entered my DSC file but in the end I get the error message: "cannot find any csd files". Here is what I entered:mri_glmfit-sim \--glmdir GLMFIT/LH_1

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

Thansk Doug. I tried it but still doesn't work. Any other thoughts? jeni ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the p

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

o track down the problem. Also, please include previous correspondence. We answer a lot of emails here, and the easier you make it on us, the faster we can solve your problem. thanks! doug On 04/25/2013 04:41 PM, Jeni Chen wrote: > Thansk Doug. I tried it but still doesn't w

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

t-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim 1GroupAvg-Cor-thickness-Mod-VAS And it did not work either. Thanks. jeni Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700 > what was your orignal mri_glmfit-sim command line? On

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

t 5:30 PM, Jeni Chen wrote: > The original command line: > > mri_glmfit-sim \ > > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > > --cwpvalthresh .999 \ > > --no-sim > > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickne

Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files

; On 2013-04-25, at 5:55 PM, Jeni Chen wrote: > Hi Doug, > > The very first command line was: > > mri_glmfit-sim \ > --glmdir > /Volumes/RainvilleHD2/Imaging_Data/Thickness/MATHIEUP_IBS/FS_1stAnalysis/GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS > \ > --sim

[Freesurfer] Directed search for group analysis

Hello Freesurfer experts, I've been trying to figure out a way to run a directed search in a group analysis. I read the tutorial on ROI analysis and some of the posts here, but we can only do it with individual subject. Simply pout, I want to restrict my search areas to 4 ROIs (determined from

[Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit

does it mean I'm 'double' smoothing my data? Jeni --- Jeni Chen, M.Sc. Agente de recherche Laboratoire de recherche en neuropsychologie de la douleur Pav. Paul-G. Desmarais, Université de Montréal CP 6128, Succ. A, Montréal, QC H3C 3J7 Tel: 514-343-6111 x4359 __

Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit

So essentially the -fwhm option in mri_glmfit does the same thing as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! Jeni ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

[Freesurfer] Thickness and variable plot in glmfit

Hello again, In Qdec we get a plot of the data for a particular vertex showing the variable and the thickness in the x, y axis respectively. Is there a way to get the same plot when using glmfit? Where do I find the data for the plot? Thank you! Jeni Chen

[Freesurfer] Freeview bus error

Hi, I was recently at the FreeSurfer workshop in Boston and learned about the "Freeview" tool in Freesurfer. However, when I tried to run it from my own laptop (Mac book pro), it crashes and gives the error message: "Bus error". I didn't get a chance to have this problem solved while I was the

[Freesurfer] Assigning multiple cores to virtual machine

Hello Everyone, I'm wondering if someone could post how to assign multiple cores to the virtual machine in the VirtualBox Ubuntu version of FS. I saw an earlier post that mentioned it but did not say how they did it. Basically we have an Intel i7 with 4 cores and 12GB of RAM. When I installed

[Freesurfer] Export table of cluster stats from Qdec

Hi, I have 2 questions regarding Qdec: 1. We would like to save the results of 'cluster stats' (the printout on the terminal after pressing the "Find clusters and go to max" button) to a text file. Is there a way to do that? Or is it automatically saved in somewhere and where would that locat