Great, thanks for the clarification Doug! Best, Alex
> > 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.
