no, that is not normal, you must have done something wrong :( On 05/09/2016 12:09 PM, Martin Juneja wrote: > 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 <mailto: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> > <mailto: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> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <mailto: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 > <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 > > > > > _______________________________________________ > 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
