Hi Yuko, The contrast only allows you to constrain the anatomical ROI. If you don't spec a contrast, then it uses the whole anat ROI. Nothing gets averaged until you run funcroi-table-sess, and that only averages over the given contrast (unless you use -vol in which case it just reports the volume of the ROI from the previous stages). Make sense?
doug Yuko Yotsumoto wrote: > Thanks Doug, > > If I don't specify a contrast with funcroi-config, then, the value I get from > funcroi-table-sess is the average across all conditions including fixation? > > What I want to get is a non-thresholded value for each condition. So I should > specify a contrast with funcroi-config, correct? > And -c flag with funcroi-config requires -sign and -thresh. So, I guess I'm > still stuck to my first question. > > >>>>> Q1) >>>>> If I don't want to use any thresholding for ROI analysis, can I use >>>>> "-sign abs -thresh 0" with funcroi-config? >>>>> > > What do you think? > Yuko > > On Dec 8, 2010, at 4:09 AM, Douglas N Greve wrote: > > >> Good point! This is a slight bug in the program that it requires a >> contrast when you ask for the volume. This is because the volume is >> completely set once you run funcroi-sess, so it won't make a difference >> what contrast you specify. The contrast only matters when you ask it to >> report a mean of a contrast. So, you can just specify any contrast in >> your analysis, or you can download a new version: >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/funcroi-table-sess >> >> I've updated the docs for this one as well. >> >> thanks >> >> doug >> >> >> Yuko Yotsumoto wrote: >> >>> Thanks Doug, >>> >>> On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote: >>> >>> >>> >>>>> I'm using: >>>>> freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 >>>>> >>>>> Q1) >>>>> If I don't want to use any thresholding for ROI analysis, can I use >>>>> "-sign abs -thresh 0" with funcroi-config? >>>>> >>>>> >>>>> >>>> Even easier: just don't specify a contrast. >>>> >>>> >>> Let me clarify. I can run funcroi-config without a contrast, but >>> funcroi-table-sess requires one. >>> Does this mean I don't specify a contrast with funcroi-config, but use -c >>> with funcroi-table-sess gives all values within the label? >>> >>> Yuko >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
