Hi Dr. Greve, Thanks for all your help. After displaying second level functional connectivity maps (actually when I display subject-wise FC maps also), I tried to match the seed region location on FC maps using tksurfer, I found that that at the seed-region partial correlation coefficient (pcc) value is not 1 and when I display sig.nii, at seed region, FC value is not signifiant. I was wondering if that's normal and freesurfer ignores self connectivity i.e. connectivity of seed region with itself or I did something wrong.
Thanks much ! On Fri, May 6, 2016 at 4:37 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Yes, those are the right commands. That will give you the ces (the > regression coefficient). Typically, people use the pearson correlation > coefficient (pcc), but I have not seen many differences between the two. > > On 05/06/2016 05:13 PM, Martin Juneja wrote: > > 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 <mailto: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 > > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://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 <mailto: > 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. > > > > > > > > > > _______________________________________________ > > 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 >
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