Thanks a lot Dr. Greve. So as per your suggestion: I ran the command isxconcat-sess -sf sessidlist -analysis workmem.sm05.rh -contrast encode-v-base -o my-group -all-contrasts i.e.- without specifying -map argument. So this generates ces.nii.gz and vesvar.nii.gz in output folder my-group. To get the significance level from 2nd level analysis, I ran mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir my-glm.wls --nii.gz
This generates sig.nii.gz file. Could you please confirm once again, that's how group level significant function connectivity is calculated from 1st level FC maps? Thanks a lot for all your help. On Fri, May 6, 2016 at 3:23 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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. > >
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