Hi Caroline
yes, you can use bbregister to register them to the surfaces derived from
the T1 (which in general is more accurate than registering directly to
the T1)
cheers
Bruce
On Mon, 16 Jun 2014, Caroline Lewis wrote:
Hi Bruce,
There's a pdt2, flair and gre. If I just run recon-all on the T1, is there a
way to register these other sequences to the T1?
Thanks,
Caroline
On Mon, Jun 16, 2014 at 2:41 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Caroline
what are the scans? If they have only 48 slices you almost
certainly
don't want to run them through recon-all. Probably you just want
to run
the 136 slice sequence and go from there.
Bruce
On Mon, 16 Jun 2014, Caroline
Lewis wrote:
> Hi Bruce,
>
> I was hoping to just do one processing, but perhaps as you
suggest that's
> not the best idea (the T1 has 136 slices whereas the other
sequences have
> 48). I have acquired these sequences to identify lesions in
some
> participants and am trying to figure out how to register/align
the other 3
> sequences to the T1.
>
> I'm also a bit confused about running preprocessing on the
scans with
> lesions. I understand that I should do the lesion tracing and
generate
> lesion maps prior to preprocessing, but am not sure how to
transform the
> lesion map to normalized space, and then run the rest of the
preprocessing.
> Do you have any suggestions?
>
> Thanks,
>
> Caroline
>
>
>
> On Mon, Jun 16, 2014 at 2:11 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
> wrote:
> Hi Caroline
>
> do you want to pocess each one independently, or are you
hoping
> to motion
> correct and average them for just one processing? If the
latter,
> you
> probably don't want to do it if the sequences are
substantially
> different.
>
> cheers
> Bruce
>
>
>
> On Mon, 16 Jun 2014, Caroline Lewis
> wrote:
>
> > Hi,
> >
> > I want to perform recon-all on four different
structural
> sequences for the
> > same participant. Three of the sequences have the same
number
> of slices,
> > whereas the T1 has fewer slices, so when I input the
different
> sequences
> > with the recon-all command, I get the following error:
ERROR:
> inputs have
> > mismatched dimensions!
> >
> > Is there a way to bypass this or make each sequence
have the
> same number of
> > slices? And if so, will this affect data quality?
> >
> > Many thanks,
> >
> > Caroline
> >
> >
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