It depends on how are you defining "percent contrast". What you are are slightly different methods.
Using -m cespct is equivalent to computing 100*Sum(contrast_i/baseline_i)/N where i is a voxel in the ROI Your method is equivalent to computing 100*Sum(contrast_i)/Sum(baseline_i) So they will be close but not exact. Which one is better? Hard to say. I would tend toward -m cespect doug On 11/01/2013 01:43 PM, Alexandra Tanner wrote: > 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 >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
