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 >> > > >> > > >> > _______________________________________________ >> > 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 >> >> >> >> > _______________________________________________ > 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. > >
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