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
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