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 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom > > it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > > in error > > but does not contain patient information, please contact the sender > > and properly > > dispose of the e-mail. > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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