Hi Doug,
Thanks, this seems to work!
Quick question -- in the past we've done ROI analyses where we've functionally constrained our labels. When calculating percent signal change we would take the output from funcroi-table-sess divide it by the output of funcroi-table-sess with no -c flag (the baseline offset value) and multiply by 100. Is this also a correct method for calculating percent signal change? I've tried it for the current ROI I'm using and compared my calculated value to the value I got by adding -m cespct and the numbers I'm getting are not the same (ex. 0.0159 vs 0.01444 for one subject). Is -m cespct more accurate? Thanks!
Best, Alex
Hi Alex, if you use "-m cespct" it will report the mean percent signal change within the ROI. Does this work? doug
On 10/31/2013 02:37 PM, Alexandra Tanner wrote:
Hi Doug and Freesurfers,
I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions:
funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg
funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED
funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix
Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated!
Thanks, Alex
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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