External Email - Use Caution Hi Freesurfer team & Doug,
Thought I would check in again about censoring volumes and using fcseedcor. I was thinking about if it hasn't been incorporated yet -- could I create my own first level covariate .dat file and run fcseedcor on a per subject basis and pass the new .dat to xreg? I assume the .dat file would be difference than the one we use for selxavg3 (currently just passing a .dat file with just a single column of a list of volumes that violate criteria). The new xreg file would have to be *m* rows long (where *m* is the number of TRs). And if frame 119, 120, and 121 where to be excluded: then it would be a *m* by 3 matrix with column 1, row 119 set to 1; row 120 column 2 set to 1; row 121 column 3 set to 1. Is that all correct? Thanks, Adam On Thu, Mar 15, 2018 at 9:47 AM, Adam Martersteck <acmar...@gmail.com> wrote: > Hi Freesurfer team & Doug, > > Just thought I'd check back in as you had asked! Any thoughts on censoring > resting state volumes for fcseedcorr? > > Thanks, > Adam > > On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Currently there is no way to do this. But it might not be hard to add. >> If I don't get back in a couple of weeks, send me a reminder. >> >> >> On 02/14/2018 12:13 PM, Adam Martersteck wrote: >> > Just a quick follow-up question, >> > For FD/DVARS or other "censoring" criteria -- using -tpexclusion >> > worked great for surface based analysis with mkanalsysis and selxavg3. >> > Is there a way to do this for seed-to-seed analysis (fcseedcor)? >> > >> > Thanks! >> > >> > On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > Yes,you need a time point exclusion file (-tpexclude filename >> > option to >> > mkanalysis-sess). Run mkanalysis with -help to get more info on how >> to >> > create it. >> > >> > On 01/25/2018 04:43 PM, Adam Martersteck wrote: >> > > Hi Freesurer experts, >> > > >> > > I’m looking to censor (drop volumes) from my resting state fMRI >> time >> > > series that violate a predetermined motion and signal threshold >> (FD >> > > and DVARS). I've already determined which volumes violate X and Y >> > > criteria. >> > > >> > > Is there a way to to tell FS to "ignore" these time points in the >> > > analysis such as in preproc-sess or mkanalysis-sess? >> > > >> > > If there is not and if I were to drop the volumes directly from >> > the 4D >> > > file before starting any pre-processing and analysis – would >> > that be >> > > a problem for finding and regressing the auto-correlation in the >> > time >> > > series? >> > > >> > > Thanks! >> > > Adam >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > 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> >> > 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 >> > <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/ >> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har >> vard.edu> >> > 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> . 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. >> > >> > >> > >> > >> > _______________________________________________ >> > 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 >> > >
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