Re: [Freesurfer] Confirming the FC steps

2016-05-09 Thread Douglas N Greve
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 >

Re: [Freesurfer] Confirming the FC steps

2016-05-09 Thread Martin Juneja
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) va

Re: [Freesurfer] Confirming the FC steps

2016-05-06 Thread Douglas N Greve
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

Re: [Freesurfer] Confirming the FC steps

2016-05-06 Thread Martin Juneja
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 t

Re: [Freesurfer] Confirming the FC steps

2016-05-06 Thread Douglas N Greve
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 finishe