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 (), but not sure if it fits. I have to use the volume scan and gii suface in matlab for local

[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 "trac

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: afn

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 wrote: > > Gree

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

Hi, I discovered that installing Freesurfer onto my local workstation and running Tkmedit from there has resolved my issue. It doesn't explain why tkmedit is so slow when run from our server, so if you have some ideas please let me know. Thank you all for your help. Best, Vy On Tue, Jun 3, 201

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

Hi! Can the connection be slow? Can you type in your local terminal and also in the ssh remote terminal the following: glxgears and let it run a while and past here the output. Cheers! Markus 2014-06-03 23:16 GMT+02:00 Vy Dinh : > Hi, > > I discovered that installing Freesurfer onto my loca

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 6

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 = 288

[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 referen

[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 longitud

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 adv

[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 muc

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 ch