Doug,

Thanks for the reply. Let me clarify two things:

1) If I don't want to use any thresholding for ROI analysis, can I use "-sign abs -thresh 0" with funcroi-config?

2) If I use thresholding, is there a way to output the number of voxels met that criteria with funcroi-table-sess?

Best, Yuko

On Dec 4, 2010, at 2:58 AM, Douglas N Greve wrote:

Currently, it is not as convenient to do this with version 5. You have to create a condition-vs-fixation for each condition that you want a time course for. Then for each condition, you need to run funcroi-table-sess for each time point (using the -frame option), then construct the waveforms from these files. It's a bit of a hassle, but scriptable.

doug

Yuko Yotsumoto wrote:

...

Hi All,

I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0

I'd like to plot HDR for each condition for each subject. With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess.

With v5.0, those commands do not seem to work.

I could get a table with:

...

funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi lh.DLPFC.roicfg -contrast all_null -sign abs -thresh 1 -force funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 funcroi-table-sess -o /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh -c all_null

However, what I want is BOLD values in each time point for all conditions. funcroi-table-sess fails if I do not specify a contrast.

...

funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi lh.DLPFC.roicfg -force funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 funcroi-table-sess -o /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh

ERROR: must specify a contrast

Is there a command that gives me values, not a table?

Thank you, Yuko

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