I'm not sure how to check the registration. I see a register.dof6.dat being produced for each run but I can't tell if it contains the correct parameters. How can I tell if the registration was accurate?
On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
did you check the registration?
On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
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 mailto: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 howlow
the threshold is? See if you get something if you set the threshclose
to 0. Does this happen in the volume and the surface? Have youchecked
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? > > 1. PREPROC > preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh > -mni305-2mm -fsd bold -per-run -stc up > > 2. SEED CONFIG > fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsdbold
> -mean -cfg mean.L_Posteriorcingulate.config > > 3. SEED TIMECOURSE > fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config > > (wm.dat and vcsf.dat were similarly created) > > 4. ANALYSIS CONFIG > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surfacefsaverage
> lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsdbold
> -TR 5 -per-run -lpf .1 > > 5. 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 > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
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