-----Msg original----- De: Giacomo Mandruzzato Enviado: 14/10/2009 06:22:24 Assunto: Re: Re: [Freesurfer] problem display tksurfer in vmware
Hi, I have a question about a probabilistic segmentation of gray matter with freesurfer. How can I do it? if I binarize like this: mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained with SPM and FSL of the gray matter? thank you in advance Giacomo 2009/9/28 Pedro Paulo de Magalhães Oliveira Junior <p...@netfilter.com.br> > Have you installed the VirtualBox that comes from the FreeSurfer Wiki? > VirtualBox 3.x? > > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.2 www.Netfilter.com.br > --- Novo Netfilter Small Business > > > > 2009/9/28 Giacomo Mandruzzato <giacomo.man...@gmail.com> > > Hi, >> now I have installed Virtual Box with freesurfer, but I have same problem >> with tksurfer and a library problem with qdec (it can't find libtiff.so.3 >> file, and in the folder I see only libtiff.so.3 file!) >> Giacomo >> >> 2009/9/26 Giacomo Mandruzzato <giacomo.man...@gmail.com> >> >> thankyou for your help and your rapid answer. >>> >>> I use bash and i set doublebufferflag=1 but the problem persists! >>> >>> >>> 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr <p...@netfilter.com.br> >>> >>>> In csh use setenv doublebufferflag 1 >>>> >>>> In bash export doublebufferflag=1 >>>> >>>> >>>> -- >>>> Enviado do meu celular Nokia E71 >>>> -----Msg original----- >>>> De: Giacomo Mandruzzato >>>> Enviado: 26/09/2009 09:33:26 >>>> Para: p...@netfilter.com.br >>>> Assunto: Re: [Freesurfer] problem display tksurfer in vmware >>>> >>>> Yes, I know but I have problem with VirtualBox in the first boot that I >>>> do! >>>> Can I use freesurfer (and so tksurfer) with vmware? Or Is there any >>>> solution >>>> for my problem? >>>> thank you >>>> >>>> 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr <p...@netfilter.com.br> >>>> >>>> > Use the official FreeSurfer distribution for Virtualbox >>>> > >>>> > -- >>>> > Enviado do meu celular Nokia E71 >>>> > -----Msg original----- >>>> > De: Giacomo Mandruzzato >>>> > Enviado: 26/09/2009 08:22:55 >>>> > Para: freesurfer@nmr.mgh.harvard.edu >>>> > Assunto: [Freesurfer] problem display tksurfer in vmware >>>> > >>>> > Hi, >>>> > I'm Giacomo Mandruzzato, a student of Bioengineering at Padova (DIE) >>>> and >>>> > I'm >>>> > working on my Thesis with Freesurfer (last version). I am using a >>>> virtual >>>> > machine Vmware 2.5.3 with Cent0S 5.1 running FSL virtual disk in >>>> Windows >>>> > Vista Home premium, >>>> > I installed freesurfer and tkmedit e qdec run correctly but when run >>>> > tksurfer (i.e. tksurfer bert rh pial, like website suggests) display >>>> an >>>> > error : >>>> > >>>> > >>>> > > [r...@localhost ~]# tksurfer bert rh pial >>>> > > surfer: current subjects dir: /usr/local/freesurfer/subjects >>>> > > surfer: not in "scripts" dir ==> using cwd for session root >>>> > > surfer: session root data dir ($session) set to: >>>> > > >>>> > > surfer: /root >>>> > > surfer: all rgb files written to /root >>>> > > surfer: Reading header info from /usr/local/freesurfer/ >>>> > subjects/bert/mri/T1.mgz >>>> > > surfer: vertices=131860, faces=263716 >>>> > > >>>> > > >>>> > > WARNING: No colortable found! >>>> > > >>>> > > >>>> > > >>>> > > surfer: single buffered window >>>> > > surfer: tkoInitWindow(bert) >>>> > > surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl >>>> > > Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl >>>> > > Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl >>>> > > >>>> > > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl >>>> > > Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl >>>> > > Successfully parsed tksurfer.tcl >>>> > > reading white matter vertex locations... >>>> > > % >>>> > > >>>> > > >>>> > >>>> > Tksurfer open and I can see only a little piece of brain. >>>> > I have update the video card's driver and I tried to use another vm, >>>> like >>>> > VirtualBox but I left the idea because I found some problem with boot >>>> of >>>> > it. >>>> > I have found a similar problem in internet, but without solution: >>>> > >>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07389.html(I<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07389.html%28I> >>>> > am not using a Nvidia video card). >>>> > >>>> > >>>> > characteristic of my notebook: >>>> > Olidata , Intel core duo T2450 @ 2 x 2.00 Ghz, >>>> > Ram 2 GB, Windows Vista Home Premium 32bit SP2 updated. >>>> > Video card: Mobile Intel 945 Express Chipset Family >>>> > >>>> > I apologize for bad English and little knowledge of Unix OS. >>>> > Please, if somebody can help I am grateful. >>>> > >>>> > Best Regards, >>>> > >>>> > Giacomo Mandruzzato >>>> > giacomo.man...@gmail.com >>>> > >>>> > >>>> >>>> >>> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
