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 <greve@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
> <greve@nmr.mgh.harvard.edu <mailto:greve@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
>     >
>     >
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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