-----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 ppj@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.mandru@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.mandru@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 ppj@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: ppj@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 ppj@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 :
[root@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(Ihttp://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.mandru@gmail.com