Re: [Freesurfer] Recommendation for Linux machine

Hi Chunchun, we have been buying opterons and running the 64 bit version of FreeSurfer, but in general, here's out advice: (1) Most important is to get something with at least 4GB RAM (2) Next make sure to buy enough disk space for your data and make sure to think about how you will

Re: [Freesurfer] regarding mkanalysis-sess.new and brainmasks

Hi Doug, hi List, On 10. Apr 2006, at 20:28 Uhr, Doug Greve wrote: I usually set it to about 20 sec (the interpretation of this parameter is that the temporal autocorrelation will return to 0 beyond this spacing). The brain mask is used to restrict the voxels overwhich the autocorrelation i

[Freesurfer] Repeated-measures in mris_glm

Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subje

Re: [Freesurfer] Repeated-measures in mris_glm

There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one "Variable". For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], w

RE: [Freesurfer] Repeated-measures in mris_glm

Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Comma

RE: [Freesurfer] Repeated-measures in mris_glm

Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem t

[Freesurfer] Curvature

How should one interpret the curvature function...what is the essence of it's being...what does it mean? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] Repeated-measures in mris_glm

I still get the same error message. Maybe I've coded the variable wrong? gdfReadHeader: reading ./test_fsgd.txt INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) <= ncols (11) Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychol

RE: [Freesurfer] Repeated-measures in mris_glm

Oh, I'm sorry. I see the problem now. When I said to create a class for each subject, I meant for each person, not for each FreeSurfer subject. So there should only be 5 classes, not 10. So do something like this: Class class_subj1 Class class_subj2 Class class_subj3 Class class_subj4 Class cla

[Freesurfer] fsfast "selxavg-sess" error

hi i am going over the fsfast tutorial. i have completed all steps up to "FsFastTutorial/905 Average session-level data by condition" https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20session_2dlevel_20data_20by_20condition when i run "selxavg-sess -sf sessid -df sessp

Re: [Freesurfer] (no subject)

Actually, if all you want to do is skullstrip on a raw volume, then you'll have to use mri_watershed by itself. Running with recon-all -skullstrip will assume that you've run the previous steps. mri_watershed can take a lot of parameters. You can look inside recon-all to see which ones we use

[Freesurfer] tksurfer - view - information - distance

tksurfer -> view -> information - >  distancewhat is the reference point for this command, ie when the cursor is on point x with a value of, say 0.02 what is that the distance of?Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

Re: [Freesurfer] fsfast "selxavg-sess" error

Add the following lines to your startup.m file FSH = getenv('FREESURFER_HOME'); fshmatlab = sprintf('%s/matlab',FSH); path(path,fshmatlab); clear fshmatlab; Paymon Hosseini wrote: hi i am going over the fsfast tutorial. i have completed all steps up to "FsFastTutorial/905 Average session-lev

Re: [Freesurfer] tksurfer - view - information - distance

It's the screen distance from the cursor or point clicked to the vertex it's reporting as the one the mouse is over or clicked. On Mon, Apr 10, 2006 at 02:09:25PM -0400, anthony gallo wrote: > tksurfer -> view -> information - > distance > > what is the reference point for this command, ie when

Re: [Freesurfer] regarding mkanalysis-sess.new and brainmasks

I usually set it to about 20 sec (the interpretation of this parameter is that the temporal autocorrelation will return to 0 beyond this spacing). The brain mask is used to restrict the voxels overwhich the autocorrelation is computed and averaged (don't want to include "air" voxels in the co

[Freesurfer] Short Course in fMRI, Spring 06

Mark Vangel and I are offering a short course in the statistical signal processing of fMRI again. April 26 & 27, 2006 7th Floor Auditorium Building 149 Charlestown Navy Yard Free, but limited to 40 attendees. Register at: http://www.nmr.mgh.harvard.edu/martinos/training/shortCoursefMRIStats.ph

[Freesurfer] Recommendation for Linux machine

Hi, We plan to buy Linux machine for freesurfer and other brain image processing. Any recommendation and related links? Thanks Chunchun ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu