I think that will work
On 4/23/18 3:08 PM, Adam Martersteck wrote:
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
<mailto: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 <mailto: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>
<mailto: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
> >
> >
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> --
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> MGH-NMR Center
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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