You should not use the sig as that is the first level significance. If you pass that to the higher level, then the results will be hard to interpret. I think you'll want to use pcc or ces. Otherwise looks ok. doug
On 05/06/2016 12:03 PM, Martin Juneja wrote: > Dear FS experts, > > I just finished calculating functional connectivity maps using > FreeSurfer. I just want to confirm if the following steps I used are > correct: > > (1). I defined configured seed regions parameters using fcseed-config > command, say R01.config and R02.config and created seeds using > fcseed-sess command to generate R01.dat and R02.dat files. > (2). Created nuisance vaiables: wm.config and vcsf.config files using > fcseed-config and -sess: this step is independent of seeds and is done > only once independent of seeds > (3). For mkanalysis-sess command for each seed using R0*.dat file, I > used '-notask' argument because I am performing resting-state analysis. > (4). For subject level analysis, I used selxavg3 for each seed > (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map sig.nii.gz > > I can process all these steps without any error. If these steps are > correct, can some one please confirm again that for RSFC, I am > correctly using -notask in step (3) and -all-contrast in step (5). > Also, in the instructions, it's mentioned to use -map pcc if > interested in calculating partial correlation coefficient, but I am > interested in using sig to get group level significant maps, would > that be OK to use in this command as -map sig? > > Thanks for your help. > > Regards, > MJ > > > _______________________________________________ > 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: 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.
