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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