Oops i just realized I only sent this to Bruce: Thanks! It looks like this involves some manual intervention. Matt., I assume you're not manually making control points on 1000s of subjects (I imagine this is for the human connectcome project). Is your code public somewhere?
Cheers, Michael On Tue, May 15, 2012 at 7:36 PM, Michael Waskom <[email protected]>wrote: > Thanks! It looks like this involves some manual intervention. Matt., I > assume you're not manually making control points on 1000s of subjects (I > imagine this is for the human connectcome project). Is your code public > somewhere? > > Cheers, > Michael > > > On Tue, May 15, 2012 at 9:14 AM, Bruce Fischl > <[email protected]>wrote: > >> sure, here's mine. Matt's is probably a lot more polished as they intend >> to run it on hundreds or thousands of subjects >> >> On Tue, 15 May 2012, Michael Waskom wrote: >> >> Hi Bruce, >>> Sounds cool, I'd be very interested in checking out the script. >>> >>> Cheers, >>> Michael >>> >>> On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl < >>> [email protected]> >>> wrote: >>> you need to call mris_make_surfaces directly. It's a bit >>> complicated as you need to intensity normalize and register the >>> hires volume to the surfaces first. I have an example script if >>> anyone is interested, but no one has used it yet but me I don't >>> think (unless Matt Glasser has gotten his version working, which >>> on second thought he probably has) >>> >>> On Mon, 14 May 2012, Michael Waskom wrote: >>> >>> Hi Bruce, >>> Is there a flag for this on recon-all? Or do you >>> need to use >>> mri_make_surfaces directly? >>> >>> Best, >>> Michael >>> >>> On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl >>> <[email protected]> >>> wrote: >>> Hi Joshua >>> >>> yes, we already have upgraded >>> mris_make_surfaces to take higher >>> res data >>> and refine the surfaces with it. Haven't tried >>> it on the aseg >>> yet, but if >>> you upload a sample dataset I could see how >>> hard it is. >>> >>> cheers >>> Bruce >>> On Mon, 14 May 2012, >>> Joshua Lee wrote: >>> >>> > Dear Freesurfers, >>> > >>> > Over the last years, MR imaging technology >>> hasimproved such >>> that sub 1-mm >>> > isotropic scans can be obtained with good >>> signal to noise >>> characteristics. >>> > For example, our lab uses 0.7mm isotropic >>> structural MR >>> images. I understand >>> > that the Freesurfer pipeline will up-sample >>> these to 1mm >>> isotropic, but it >>> > seems a shame that so much information is >>> left unused which >>> could be used to >>> > improve the accuracy of sub-cortical and >>> cortical >>> segmentation. My question >>> > is whether there are any plans at Freesurfer >>> to change the >>> reference >>> > standard resolution from 1mm isotropic, or >>> provide another >>> solution that can >>> > help researchers make the most of your >>> technology. >>> > >>> > Sincerely, >>> > >>> > >>> > Joshua >>> > - >>> > Joshua >>> > >>> > >>> > >>> ______________________________**_________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>> freesurfer<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<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 [email protected] 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.
