Re: [Freesurfer] Abblocked Setup

2011-02-09 Thread Douglas N Greve
Chindhuri Selvadurai wrote: > Dear Doug, > > Thanks for your response! > > Our stimuli starts with the null condition, but abblocked assumes it's the > ON condition. Is there a way to invert this? > No, not currently, though you can tell tkmedit/tksurfer to invert the color scale. Or you can

Re: [Freesurfer] Abblocked Setup

2011-02-08 Thread Chindhuri Selvadurai
Dear Doug, Thanks for your response! Our stimuli starts with the null condition, but abblocked assumes it's the ON condition. Is there a way to invert this? When we look at the sig maps, how do we know what the contrast is? Which condition does it think is null/task, negative/positive? From what

Re: [Freesurfer] Abblocked Setup

2011-02-07 Thread Douglas N Greve
sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: > Hi Doug, > > For some reason, our mkanalysis-sess command only created an > analysis.info file and not a .cfg file, so we can't run the abblocked > analysis using sfa-sess. Do you know

Re: [Freesurfer] Abblocked Setup

2011-02-07 Thread Chindhuri Selvadurai
Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command

[Freesurfer] abblocked Setup

2011-02-07 Thread Chindhuri Selvadurai
Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions wi

Re: [Freesurfer] Abblocked Setup

2011-02-07 Thread Douglas N Greve
The contrasts are going to be created automatically. These will be: fund - stands for "fundamental" - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of

[Freesurfer] Abblocked Setup

2011-02-07 Thread Chindhuri Selvadurai
Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions wil