Re: [Freesurfer] GLM design question

2012-01-11 Thread Martijn Steenwijk
Dear Doug, Michael, Thanks for thinking with me. Following the discussion, it seems to me that weighting the contrast matrix in our cohort for our question is alright. Let me describe it again: - The diseased population typically consists of 75% female. - We have three groups (HC, diseased withou

[Freesurfer] Non_FA Group study

2012-01-11 Thread Antonella Kis
Dear FS team, Can use my results from the mri_cvs_register to do a non_FA group analysis, more exactly I am interested on the mean diffusivity (adc.nii from dt_recon). Since from the significant map I can only find the p values how can I see if there is an increase or decrease of the FA va

Re: [Freesurfer] Non_FA Group study

2012-01-11 Thread Bruce Fischl
sure, that should be straightforward. cheers Bruce On Wed, 11 Jan 2012, Antonella Kis wrote: > > Dear FS team, > > > Can use my results from the mri_cvs_register to do a non_FA group analysis, > more exactly I am interested on the mean diffusivity (adc.nii from > dt_recon). > > > Since from

Re: [Freesurfer] Non_FA Group study

2012-01-11 Thread Antonella Kis
Dear Bruce, Many thanks for your reply and your help. Can you please give me an advise on how I can do a comparison between two groups for my FA data or in other words for FA group analysis since from the significant map I can only find the p values how can I see if there is an increase or

Re: [Freesurfer] Building from source without GUIs

2012-01-11 Thread Nick Schmansky
malcolm, hi, i'm able to replicate that warning on that data, and i'm investigating. i would say its a false alarm, as that input data is considered 'optimal' (mprage from our own scanners). it appears the recon-all proceeded successfully all the way to nearly the end. it failed in some new co

Re: [Freesurfer] Building from source without GUIs

2012-01-11 Thread Malcolm Tobias
Nick, On Wednesday 11 January 2012 11:52:19 Nick Schmansky wrote: > it appears the recon-all proceeded successfully all the way to nearly > the end. it failed in some new code (you are working with our > 'development' checkout, so new stuff often breaks the stream), so i'll > have to pass that

Re: [Freesurfer] Non_FA Group study

2012-01-11 Thread Antonella Kis
Dear Bruce, Once again many thanks for helping.I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register.  I used the GLM group analysis method after I concatenate FA from individuals into one file and used mri_glmf

[Freesurfer] FA group analysis

2012-01-11 Thread Antonella Kis
Dear Bruce, Once again many thanks for helping.I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register.  I used the GLM group analysis method after I concatenate FA from individuals into one file and used mr

[Freesurfer] Selxavg3-sess Out of Memory - What are the options?

2012-01-11 Thread SHAHIN NASR
Hi, I am running selxavg3-sess under freesurfer 4.5 and I faced "out of memory error" as it started "computing whitening matrices". Since they are monkey datasets, runs were relatively long (12 runs each 16 min; TR=1.4). I want to know what options do I have here? Please note that, when I appl

Re: [Freesurfer] 'fsaverage' directory

2012-01-11 Thread swoodman
Thank you! > sandra, > > the two fsaverage's that you are using are the same. you can change one > of the links to point at the other if you prefer, or continue to use it > as-is. it will not affect the results. > > n. > > > On Tue, 2012-01-10 at 15:10 -0500, swood...@nmr.mgh.harvard.edu wrote:

Re: [Freesurfer] watershed error in skull strip routine

2012-01-11 Thread Bruce Fischl
Hi Tim that's a new error - congratulations! If you upload the dataset I'll take a look, but I suspect if you add some control points it will work fine. cheers Bruce On Wed, 11 Jan 2012, Holden, Timothy wrote: Hi FS experts,   I?m encountering an error in the Skull Strip routine with