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
