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 <fischl@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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