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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 acmarter@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 < greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 howto
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 fMRItime
> 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 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 <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:Freesurfer@nmr.mgh.harvard.edu>
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