Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

Hi Nick, again thank you your help! That works nicely. Where to I find the transformation matrix to register my structural volume data to the gii. surface file? I found two matrices in the lh.white.gii (MatrixData), but not sure if it fits. I have to use the volume scan and gii suface in

[Freesurfer] TRACULA statistics by mri_glmfit

Hi list, I'm comparing TRACULA results on three groups.I need to add age as covariate.Therefore, I I'd like to use mri_glmfit for TRACULA statistics but I'm confused on command line.Specifically, from tutorial --y inputfile can be volume or surface-based but my TRACULA results come form

Re: [Freesurfer] TRACULA statistics by mri_glmfit

Use --table instead of --y doug On 6/3/14 6:43 AM, std...@virgilio.it wrote: Hi list, I'm comparing TRACULA results on three groups. I need to add age as covariate. Therefore, I I'd like to use mri_glmfit for TRACULA statistics but I'm confused on command line. Specifically, from tutorial

[Freesurfer] Fwd: How to improve/fix TKMEDIT lag

Greetings Freesurfer developers, I'm looking for ways to improve the speed of TKMEDIT for Freesurfer 5.3. Specifically, the GUI interface is abnormally slow; edits made to a voxel takes 1-2 seconds to show up on the screen. Interesting, the recon-all doesn't appear to be slow (as each subject has

[Freesurfer] 3dvolreg Error for preproc-sess

Hi all, I'm running version 5.2 off-site, and I keep running up against an error for preproc-sess. From my SUBJECTS_DIR, I am running preproc-sess -fsd bold -s 608_Sess1 -fwhm 5 -per-run which provides the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol:

Re: [Freesurfer] Fwd: How to improve/fix TKMEDIT lag

Hi, What machine are you actually running tkmedit on? more specifically: You appear to be using a mac. Do you run tkmedit directly on the mac? or are you using ssh -X (or something like it to run it) on the Red Hat machines? Thanks, D On Tue, Jun 3, 2014 at 11:55 AM, Vy Dinh vdi...@wisc.edu

Re: [Freesurfer] Fwd: How to improve/fix TKMEDIT lag

Hi Markus, Thanks for your help! Here's what I have after typing glxgears: 16523 frames in 5.5 seconds = 3013.267 FPS 362 frames in 5.4 seconds = 66.654 FPS 367 frames in 6.5 seconds = 56.306 FPS 381 frames in 277.1 seconds = 1.375 FPS 16640 frames in 5.2 seconds = 3201.886 FPS 262 frames in

Re: [Freesurfer] Fwd: How to improve/fix TKMEDIT lag

Hi Vy, This is what my 2011 MBP gives: $ glxgears 10235 frames in 5.0 seconds = 2046.978 FPS 10612 frames in 5.0 seconds = 2122.353 FPS 10689 frames in 5.0 seconds = 2137.778 FPS 14639 frames in 5.0 seconds = 2927.775 FPS 14584 frames in 5.0 seconds = 2915.777 FPS 14437 frames in 5.0 seconds =

[Freesurfer] ?reference(s) supporting DLPFC label

Dear FS community, I'm looking into DLPFC volume/thickness. Following advice posted before on this forum, I'm adding G_frontal_middle.label + S_frontal_inferior.label + S_frontal_middle.label from Destrieux 2009 atlas as a surrogate for DLPFC. My question is whether folks could provide

[Freesurfer] Advice - best method, longitudinal vs. cross-sectional

Hello Everyone, could someone please give us an advice about which method you consider is the best for our study ? we have two groups with MRI at Time 1. Each group received medication. After this we performed another MRI at Time 2 after 2 weeks. The best method for this study is a

Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

Hi Alex I would think that longitudinal analysis is still the way to go as we try to improve both reliability and sensitivity using the fact that we have multiple scans/subject. cheers Bruce On Tue, 3 Jun 2014, Alexandru Hanganu wrote: Hello Everyone, could someone please give us an

[Freesurfer] TRACULA: Exits with Errors, and ERROR in -qa Flag

Dear Anastasia, I wrote to the Freesurfer Listserv yesterday about the problem I am facing in running tracula, although my FS is set to version 5.3. However, I debugged some problems in the config file, and now trac-all -prep runs through all the DTI volumes, but exits with errors. Also, it does

Re: [Freesurfer] ?reference(s) supporting DLPFC label

Kev, I can't speak so much to the method you describe in your e-mail, but for my work I've taken a different approach, owing to certain structures not currently being parcellated in Freesurfer. Of course, in this case I think that's because the DLPFC isn't really well defined, anatomically, as

Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

Hi Alex, The time distance does not matter. It's best to use a longitudinal method (both for the image processing, to reduce noise, and for the statistics, to gain power).  Your design seems to be missing a control group (unless one off your groups is placebo). In your design you can compare