Hi Doug, I was able to get the surface connectivity analysis to run successfully for the L.Cingulate example that you posted online ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough ). For my own analysis, I'm hoping to use my own functionally defined ROIs instead of freesurfer segmented regions. For that, do I pass a vol2surf command on my spherical ROIs and then run the same analysis? I saw that to prepare a ROI for this kind of analysis, I need to create a configuration file using funcroi-config, but this command seems to use anatomical ROIs based on freesurfer segmentation again.
Could you advise how to proceed? Thanks, Jiahe On Mon, Aug 11, 2014 at 5:18 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did not do > this, try it > > tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t > fmcpr.up.sm6.fsaverage.lh.nii.gz > > This will bring up an overlay as well as a time course > > > On 08/11/2014 05:05 PM, Jiahe Zhang wrote: > > Both looked fine. First value in .mincost is .45 > > > > > > On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > two ways: > > > > 1. run tkregister-sess to visually check them > > 2. look at the first value in register.dof6.dat.mincost. It is hard > to > > say what a threshold is for a good registration, but typical > > values are > > about .5 or so. If it is .8 or more, it is probably a problem (and > > probably the initialization is not good) > > > > > > On 08/11/2014 04:35 PM, Jiahe Zhang wrote: > > > 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 > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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 > > > > <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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/FsFastFunctionalConnectivityWalkthrough > ). > > > > > 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 > > > -fsd bold > > > > > -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 > > -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 > > > > > > > > > > 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> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto: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 > > > > gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >>> > > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > > <tel:617-724-2358>>> > > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://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> > > > <http://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> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > The information in this e-mail is intended only for the > > > person to > > > > whom it is > > > > addressed. If you believe this e-mail was sent to you in > > > error and > > > > the e-mail > > > > contains patient information, please contact the Partners > > > > Compliance HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was > > sent to > > > > you in error > > > > but does not contain patient information, please > > contact the > > > > sender and properly > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > -- > > > > Jiahe Zhang > > > > Ph.D. Student > > > > Department of Psychology > > > > Northeastern University > > > > 617-373-4789 <tel:617-373-4789> <tel:617-373-4789 > > <tel:617-373-4789>> > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto: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 > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel: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> > > > <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> > > > <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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > -- > > > 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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 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> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Jiahe Zhang > > Ph.D. Student > > Department of Psychology > > Northeastern University > > 617-373-4789 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789
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