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 fischl@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 <fischl@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 <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 > > > > > _______________________________________________ > 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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