I would suggest you to check if preproc is done using the argument -mni-305-2mm.
On Wed, May 11, 2016 at 12:48 PM, Sahil Bajaj <sahil.br...@gmail.com> wrote: > Hi Dr. Greve, > > This works for me if I define seeds into subject-wise anatomical space. > > Now, location of seed regions across subjects might differ because these > are defined in subject-wise anatomical space. Hence subject-wise > connectivity maps are generated from subject-wise seeds but these can be > displayed only on fsaverage space, not on subject-wise space. That means > connectivity maps are normalized here and we can do 2nd level analysis > (keeping subject-wise seeds as subject-wise (not normalized)). > > (a). If above points are correct, then it's fine to calculate 2nd level > maps but I am not sure how seeds can be overlaid on 2nd level maps or 1st > level maps because seeds are not normalized but both 1st and 2nd level > connectivity maps are. Is there any way I can make sure that self > connectivity is giving correlation coefficient ~1. > (b). If above points are incorrect i.e. if subject-wise connectivity maps > are not normalized and are in subject-wise space then (i) why can't we > overlay those on subject-wise connectivity maps on subject-wise surfaces > and (ii) how second level maps can be calculated from un-normalized > 1st-level level maps? > > For second level analysis, I am using isxconcat-sess and mri_glmfit. > > Could you please clarify this for me? > > Thanks, > Sahil > > On Tue, May 10, 2016 at 10:44 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> You should map the ROI into the individual subject's anatomical space, >> the specify the ROI when you configure the seed (eg, fcseed-config -seg >> ROI.mgz -segid 1 ...) >> >> On 05/10/2016 10:37 AM, Sahil Bajaj wrote: >> > Hello all, >> > >> > I am interested in importing some seed regions which are in MNI space >> > in order to calculate functional connectivity maps. Looks like command >> > preproc-sess doesn't normalize the BOLD data and only the regions >> > generated by FreeSurfer LookUp table which have 'segid', can be used >> > to calculate functional connectivity maps. >> > >> > I was wondering how can I normalize the BOLD and T1w data so that I >> > can use >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough >> > instructions to calculate functional connectivity from MNI seed regions. >> > >> > Thanks, >> > Sahil >> > >> > -- >> > ------------------------------------------------- >> > Sahil Bajaj >> > Post-doctoral Fellow >> > Nantz National Alzheimer's Center, Department of Neurology >> > The Houston Methodist Research Institute (THMRI) >> > Houston, TX, USA. >> > E-mail:sahil.br...@gmail.com <mailto:e-mail%3asahil....@gmail.com> >> > >> > >> > _______________________________________________ >> > 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 >> >> >> 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. >> >> > > > -- > -- > ------------------------------------------------- > Sahil Bajaj > Post-doctoral Fellow > Nantz National Alzheimer's Center, Department of Neurology > The Houston Methodist Research Institute (THMRI) > Houston, TX, USA. > E-mail:sahil.br...@gmail.com <e-mail%3asahil....@gmail.com> > > _______________________________________________ > Freesurfer mailing list > 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. > >
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