Re: [Freesurfer] Confirming the FC steps

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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