Hi Doug, I use the following command for fslmaths fslmaths fmc.nii -bptf 200 2 fmcfilt.nii
where 200*(TR+2) is 400s, and 2*(TR=2)=4s. and for mkanalysis-sess -force -fsd bold -funcstem fmcfilt -analysis name -notask -tr 2 -runlistfile name -native -nskip 5 -mask brain -tpef name -taskreg name for debugging, I did not include nuisance regressors. Caspar 2012/5/7 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > What frequencies did you chose for the FSL bandpass filter? What is you > mkanalysis-sess command? > > > On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote: > >> yes >> >> 2012/5/7 Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> >> Did you regenerate the seeds after filtering? >> >> >> On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote: >> >> I have tried analyses with only one seed time course (either 1 >> voxel, mean of a sphere of 1 voxel radius, or mean of a >> functionally defined roi), as well as several seeds within the >> same design matrix, with the same problem. >> All of these analyses did yield higher pcc when done without >> filtering. >> Caspar >> >> 2012/5/7 Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard. edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> >> >> Is this doing all of those seeds simultaneously or one seed >> at a time? >> >> On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote: >> > Hi, >> > I am trying to use fslmaths to filter my data before I plug it >> into a >> > resting state analysis. However, once I obtain a pcc map, all >> > correlation coefficients are <0.1, even the autocorrelation >> with the >> > seed voxel. >> > The data look fine when I open them in Matlab using MRIread; the >> > correlations between individual voxel time courses obtained in >> Matlab >> > is about 0.6. >> > >> > My analysis stream is as follows: >> > a) I filter the data using "fslmaths input -bptf highpass >> lowpass >> > output"; from this I obtain a filtered nii.gz file >> > b) I extract a seed timecourse from the filtered data in Matlab >> > c) I run mkanalysis-sess with -notask >> > d) I run selxavg3-sess >> > e) I overlay the pcc.nii >> > >> > I have tried this with smoothed and unsmoothed data, with and >> without >> > nuisance regressors, with different seeds, with mri_convert >> after step >> > a. It is not a problem with the overlay since the max values >> in pcc >> > are all <0.1. >> > I noticed that there are some differences in the nifti header >> (as read >> > with MRIread) before and after filtering, but it seemed to >> me that >> > they are gone after I used mri_convert. >> > I do find much higher correlations with unfiltered data. >> > Any advice what could be going wrong here? I am using >> Freesurfer 5.1 >> > and FSL 4.1.9 on Linux. >> > Thanks, Caspar >> > >> > >> > >> > ______________________________ _________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> <mailto:freesur...@nmr.mgh. harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ >> freesurfer >> >> >> <https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard. edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu <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> <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 >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> >> FileDrop: 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 >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> ______________________________ _________________ >> >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> <mailto:freesur...@nmr.mgh. harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer >> >> >> <https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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 >> >> <http://www.partners.org/**complianceline<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. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: 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> >> > >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
_______________________________________________ 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.
