Re: [Freesurfer] mris_preproc --fsgd

Thanks Doug, here is the preproc log using the debug option: nmr. set echo = 1 ; set debug = 1 ; set debug = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 10 != 0 ) set flag = $argv[1] ; shift ; set flag = --fsgd shift switch ( $flag ) switch ( --fsgd ) if ( $#argv == 0 ) goto

Re: [Freesurfer] Testing Freesurfer Installation- Errors

Hi Melissa we need to know more about your environment. What kind of machine are you running on? Are you running it directly on the terminal, or using some type of remote access or virtual machine? cheers, Bruce On Wed, 12 Sep 2012, Melissa Lancaster wrote: Hi, It seemed I had

Re: [Freesurfer] Testing Freesurfer Installation- Errors

Hi Missy, yes, that sounds like at least part of your problem. What trouble did you have sourcing our env file? Can you send us the screen output? Bruce On Wed, 12 Sep 2012, Melissa Lancaster wrote: Hi again- I should have added that I am using Mountain Lion. I have downloaded Quartz and

Re: [Freesurfer] Testing Freesurfer Installation- Errors

Dr. Fischl, Thanks so much. Unfortunately, I had closed the window. But here is what happened: I set the environment: setenv FREESURFER_HOME /Applications/freesufer However, after typing the next command: source $FREESURFER_HOME/SetUpFreeSurfer.csh I got the following error:

Re: [Freesurfer] multicenter morphometric analysis

Thanks Doug and Bruce Does anyone have an opinion regarding the necessity of scanning the ADNI phantom? Best wishes Heath On Wed, Sep 12, 2012 at 1:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: If you include scanner as an interaction nuisance variable and balance your design so

Re: [Freesurfer] head motion values

Hi New Fei, I did some digging and found the docs for the output (pasted below). Translations (displacement) are in mm, rotations are in degrees doug 1. n : time point 2. roll : rotation about the I-S axis (degrees CCW) 3. pitch : rotation about the R-L axis (degrees CCW) 4.

Re: [Freesurfer] mris_preproc --fsgd

Are you sure that oa_txeffect_verum.fsgd has more than two subjects? This run seems different than the one you sent yesterday which only found one subject. doug On 09/13/2012 08:48 AM, spa...@nmr.mgh.harvard.edu wrote: Thanks Doug, here is the preproc log using the debug option: nmr. set

Re: [Freesurfer] multicenter morphometric analysis

Is that the one used to measure distances? If you have it, it's probably not a bad idea. If all your scanners have the same metric, then that's good, though it is not clear what you do post hoc with the information if they don't. doug On 09/13/2012 10:57 AM, Heath Pardoe wrote: Thanks Doug

Re: [Freesurfer] Choroid Plexus in ventricles

Hi. Thanks for the response below. Does the fact that choroid plexus varies so much in intensity mean that Freesurfer does not always accurately measure CP volume? Do you think we should do some manual tracing to confirm Freesurfer results? Thanks, Tracy From: Bruce Fischl

Re: [Freesurfer] Choroid Plexus in ventricles

Hi Tracy I guess so. We haven't quantified it at all. cheers Bruce On Thu, 13 Sep 2012, Tracy A. Butler wrote: Hi. Thanks for the response below. Does the fact that choroid plexus varies so much in intensity mean that Freesurfer does not always accurately measure CP volume? Do you think

Re: [Freesurfer] head motion values

Hi Doug, Can you point out the name of file that I should be looking at? I assumed they were either the mcextreg and mcprextreg output files, but these only have 6 columns. Thanks, New Fei Hi New Fei, I did some digging and found the docs for the output (pasted below). Translations

Re: [Freesurfer] head motion values

Either fmcpr.mcdat or fmc.mcdat On 09/13/2012 02:07 PM, New Fei Ho wrote: Hi Doug, Can you point out the name of file that I should be looking at? I assumed they were either the mcextreg and mcprextreg output files, but these only have 6 columns. Thanks, New Fei Hi New Fei, I did some

Re: [Freesurfer] mris_preproc --fsgd

Yes, it still has 22 subjects. The only difference between yesterday and today was that I individually ran mris_preproc on subjects 005, 006, 007, and 010 to test whether any of those files were corrupt or missing. All 4 successfully ran mri_surf2surf, however this morning when I ran mris_preproc

[Freesurfer] Freeview display errors - Ubuntu 12.04

Hi Freesurfers, I've recently moved onto Ubuntu 12.04. The Freesurfer installation has required me to download various libraries and create many symbolic links to have it working. Further more I've had to set the doublebufferflag=1 (whatever that is) in order for tkmedit and freeview to work

Re: [Freesurfer] mris_preproc --fsgd

Something very strange is going on. What platform are you using? What version of FreeSurfer? Can you send me the fsgd file as an attachment instead of pasting it into email? doug On 09/13/2012 03:58 PM, spa...@nmr.mgh.harvard.edu wrote: Yes, it still has 22 subjects. The only difference

[Freesurfer] Anatomical variation between individual surface and average template

Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by