Hi Stefanie -

What we heard previously from ENM is that there is a bug in the
maxfilter utility - perhaps this is preventing it from doing what you
want. Also, I suspect that running tsss may automatically remove all
the information about the head movements as it contaminates the
signal, so a later movement correction may not be possible.

We have not noticed the problem with noise after movement correction
(although we have not had much experience with this so far), but this
sounds serious - I am afraid we have to wait until one of the
developers gets back to us about this when the holidays season in
Helsinki is over ;-(

cheers,
yury

2007/7/26, Hassel, Stefanie <[log in to unmask]>:
> Hi Yury,
>
> Thanks for getting back on this … yes, I think you are right it would be
> best to do artefact correction and head transform in one step.
>
> The problem is twofold:
>
> 1) I already have a number of datasets where I only applied tsss. As it is
> time-consuming (it seems to run a fair while at least on our machine), I had
> hoped to do the transformation separately on the already maxfiltered data.
>
>
>
> 2) - this I find far more concerning: for a recent subject I applied both
> steps in one go, but the output file was still quite noisy. So, I run tsss
> without head-transform and the data was a lot better … that I found odd and
> wanted to compare it to the output I would get from running head transform
> on an already maxfiltered dataset.
>
> I would need the –nosss option (it does not work when input file is already
> maxfiltered) plus the –trans option and that somehow does not work. The
> error messages are from can't read input file to command not known …
>
>
>
> I hope this makes sense. I wonder have you noticed difference in the
> "noise-level" of your data when running tsss + head transform vs tsss alone?
>
>
>
> stefanie
>
>
>
> Stefanie Hassel, PhD
>
> Functional Neuroimaging in Emotional Disorders,
>
> Department of Psychiatry,
>
> Western Psychiatric Institute and Clinic,
>
> University of Pittsburgh
>
> Loeffler Building,
>
> 121, Meyran Avenue,
>
> Pittsburgh. PA 15213.
>
>
>
> Phone: (+1) 412-383-8193
>
>  Fax: (+1) 412-383-8335
>
>
>
>
>
>
> -----Original Message-----
>  From: [log in to unmask] [mailto:[log in to unmask]] On
> Behalf Of Yury Shtyrov
>  Sent: Thursday, July 26, 2007 8:56 AM
>  To: Hassel, Stefanie
>  Subject: Re: maxfilter: head transform after tsss
>
>
>
> Wouldn't it be better to run it on the original raw data along with
>
> tsss extension? Otherwise, if it  attempts to apply sss for the second
>
> time, it  is probably not good. What is the program's feedback? It
>
> probably sees the file has been sss-ed and stops there. You could
>
> probably try it with nosss option, but then it will probably refuse to
>
> do the transform.
>
>
>
> yury
>
>
>
> 2007/7/25, Hassel, Stefanie <[log in to unmask]>:
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > dear all,
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > i wondered if it is possible - using maxfilter - to do the Move --> head
>
> > transform (to default) after having already applied tsss.
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > i have tried running it separately from the command line
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >    maxfilter -trans <data_tsss.fif> | default
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > but it does not seem to work.
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > any advice would be very much appreciated.
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > many thanks,
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > stefanie
>