Try this version https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_convert
On 05/03/2018 03:05 AM, Klink-3, N.E.C. van wrote: > External Email - Use Caution > > Unfortunately no, same shift and rotation. > And in addition messed up vertices... > > > Nicole > > -----Oorspronkelijk bericht----- > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N. Greve > Verzonden: 3 mei 18 0:08 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] combinesurfs problem: shifts and rotates > > Does it work if you don't save it as an stl file? > > > On 05/02/2018 06:39 AM, Klink-3, N.E.C. van wrote: >> >> Dear all, >> >> I am struggling with coverting and combining pial surfaces back to >> native space. My result is 90 degrees rotated, and shifted from the >> original MRI. >> >> The initial lh.pial and rh.pial look good, and when I translate them >> to native space they still look good. However when I combined them, >> they suddenly shift and rotate. Does anyone know what happens, how I >> can prevent it, or reliably can shift and rotate back? >> >> Also, if I do not save directly to STL, the surfaces get messed up in >> -combinesurfs, with a lot of vertices shifted to the center of the >> surface (see picture below). But this is not my biggest problem, as I >> want STL in the end. >> >> My code: >> >> /tkregister2 --mov rawavg.mgz --targ orig.mgz --reg >> register.native.dat --noedit -regheader/ >> >> // >> >> /mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz >> --tval lh.pial.native --tval-xyz --hemi lh --s {SUBJECT}/ >> >> /mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz >> --tval rh.pial.native --tval-xyz --hemi rh --s {SUBJECT}/ >> >> // >> >> /mris_convert --combinesurfs >> $SUBJECTS_DIR/${subject}/surf/lh.pial.native >> $SUBJECTS_DIR/${subject}/surf/rh.pial.native >> $SUBJECTS_DIR/bh_native.stl/ >> >> Thanks in advance, >> >> Nicole >> >> ---------------------------------------------------------------------- >> -- >> >> /De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is >> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht >> onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de >> afzender direct te informeren door het bericht te retourneren. Het >> Universitair Medisch Centrum Utrecht is een publiekrechtelijke >> rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en >> Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van >> Koophandel voor Midden-Nederland onder nr. 30244197. / >> >> /Denk s.v.p aan het milieu voor u deze e-mail afdrukt. / >> >> ---------------------------------------------------------------------- >> -- >> >> /This message may contain confidential information and is intended >> exclusively for the addressee. If you receive this message >> unintentionally, please do not use the contents but notify the sender >> immediately by return e-mail. University Medical Center Utrecht is a >> legal person by public law and is registered at the Chamber of >> Commerce for Midden-Nederland under no. 30244197. / >> >> /Please consider the environment before printing this 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. > > > > _______________________________________________ > 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
