There's nothing even when the threshold is set to 0.
I just checked the preprocessing outputs. I can see normal-looking volumes fmcpr.nii.gz fmcpr.up.nii.gz fmcpr.up.sm6.mni305.2mm.nii.gz
But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or fmcpr.up.sm6.fsaverage.rh.nii.gz
On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
When you say that they are "empty" what do you mean? That there is nothing above threshold or that there is nothing regardless of how low the threshold is? See if you get something if you set the thresh close to 0. Does this happen in the volume and the surface? Have you checked the registration to assure that it is accurate?
On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
Hi Doug,
I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr... ).
I was able to successfully run the following commands (nothing errored as far as I can tell) but the resulting partial correlation and significance maps turned out to be empty. Could you take a look at the commands and let me know if anything can be improved?
- PREPROC
preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh -mni305-2mm -fsd bold -per-run -stc up
- SEED CONFIG
fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config
- SEED TIMECOURSE
fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config
(wm.dat and vcsf.dat were similarly created)
- ANALYSIS CONFIG
mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 5 -per-run -lpf .1
- ANALYSIS
selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001
Thanks, Jiahe
-- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789
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