give it one slice in every dicom series and it will figure out the rest. If
you specify more than one series (with more than one -i <dicom slice> it
will do motion correction and averaging.
cheers
Bruce
On Tue, 17 Jun 2014, Caroline Lewis wrote:
Thanks Bruce. Also for running recon-all on the T1 - in terms of motion
correction, is it better to run it with one nifti file converted from all
the dicoms (therefore 1 input), or all of the dicom files (if this is even
possible)?
Caroline
On Mon, Jun 16, 2014 at 2:58 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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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