Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

Re: [Freesurfer] Summing ROIs on fsaverage surface
by oliver hinds 28 Sep '09

28 Sep '09

hi holly, you can average labels in a common surface space with mris_spherical_average. when you say you used mri_surf2vol, though, it sounds like you have these labels in volume space? good luck, oliver Holly Bridge wrote: We have an ROI for V1 of each of 10 subjects that we have transformed onto the surface of fsaverage with mri_surf2vol. Now we would like to sum these binary masks to produce a single mask with values from 0 to 10 corresponding to the overlap of the individual masks on the average surface. Is there a way to do this with freesurfer tools or do we need to invoke fslmaths from the FSL tools? Thanks, Holly --------------------------------------------------------------------------------------------------- Dr Holly Bridge Royal Society University Research Fellow FMRIB Centre Tel: +44-1865-222582 John Radcliffe Hospital Headington Oxford OX3 9DU Email: hb(a)fmrib.ox.ac.uk Lecturer and JRF, New College

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autorecon2 error
by Ahmed, F, Me <fahmed＠sun.ac.za> 28 Sep '09

28 Sep '09

Hello, I tried testing out my Fs by creating a new subject directory "ernie" as instructed by the ReadMe file in the "Subjects" folder in Fs, I successfully created the subjects directory for "ernie" and successfully ran autorecon1, I then wanted to try and run autorecon2 for this subject, but it exited with errors. I have attached the recon-all log for this. I hope someone could possibly help. Kind regards

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mri_label2label --regmethod question
by Stefan Ehrlich 28 Sep '09

28 Sep '09

Hi there, I copied fsaverage into my SUBJECTS_DIR, opened it with tksurfer, drew a custom label on the fsaverage surface and saved it under labels. I then used mri_label2label to map this new label to individual subjects with the --regmethod surface flag : mri_label2label --srclabel /.../subjects/fsaverage_local/label/lh.NEW.label --srcsubject fsaverage_local --trglabel lh.NEW_C.label --trgsubject M222 --regmethod surface --hemi lh Does the --regmethod surface take care of the different spaces my source and target images are in (e.g.M222 above is in native space I assume)? Thanks, Stefan

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Fwd: Re: problem display tksurfer in vmware
by Pedro Paulo de Magalhães Oliveira Junior 28 Sep '09

28 Sep '09

---------- Forwarded message ---------- From: Giacomo Mandruzzato <giacomo.mandru(a)gmail.com> Date: 2009/9/28 Subject: Re: Re: [Freesurfer] problem display tksurfer in vmware To: Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> ok.thank for interest. I resolved my problem: -I installed Virtual Box -tksurfer: I need to DISABILITATED 3D accelerator graphic in configuration video of virtual box -qdec:reboot in kernel configuration, overwrite password for user 'freesurfer', and so I can create link for libtiff.so.4 named libtiff.so.3 Now run correctly, I have to wait about 1 second every rotation for tksurfer with subject bert , but I think it so good. thank you very much for your answer 2009/9/28 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)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(a)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(a)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(a)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(a)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(a)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(a)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(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.mandru(a)gmail.com >>>> > >>>> > >>>> >>>> >>> >> >

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Re: [Freesurfer] problem display tksurfer in vmware
by Pedro Paulo de Magalhães Oliveira Junior 28 Sep '09

28 Sep '09

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(a)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(a)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(a)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(a)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(a)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(a)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(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.mandru(a)gmail.com >>> > >>> > >>> >>> >> >

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RES: Re: problem display tksurfer in vmware
by Pedro Paulo de Magalhaes Oliveira Jr 26 Sep '09

26 Sep '09

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(a)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(a)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(a)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(I > 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(a)gmail.com > >

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RES: problem display tksurfer in vmware
by Pedro Paulo de Magalhaes Oliveira Jr 26 Sep '09

26 Sep '09

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(a)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 (I 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(a)gmail.com

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problem display tksurfer in vmware
by Giacomo Mandruzzato 26 Sep '09

26 Sep '09

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 (I 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(a)gmail.com

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question abt mri_surf2surf usage
by Ritobrato Datta 25 Sep '09

25 Sep '09

Hello All, I am confused abt the sage of mr_surf2surf. I have 3 subjects. All three have been piped through freesurfer autorecon-all. So i have subj? ?h sphere.reg I also have functional data for the 3 subjects overlaid on the subj? ?h sphere.reg and I saved them as .mgh files. I want to map subj2.mgh and subj3.mgh to subj1 ?h sphere.reg How do I do that ? I looked at the mri_surf2surf usage but got confused. Please let me know. Thanks a lot Ri

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Re: [Freesurfer] Perirhinal cortex
by Jose Luis Cantero Lorente 25 Sep '09

25 Sep '09

Hi there, thanks for your responses. Indeed, what we need is to get thickness values for the entorhinal, perirhinal, and the rest of the parahippocampal cortex, separately. Is that feasible by using Freesurfer release 4.02? I would appreciate your help with this issue. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/ ----- Mensaje original ----- De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Fecha: Viernes, Septiembre 25, 2009 5:21 pm Asunto: Re: [Freesurfer] Perirhinal cortex > all of parahippocampal together you mean? We have entorhinal > probability > maps already and should have perirhinal soon, and I think Rahul > already has > a parahippocampal (separate from entorhinal) label > > On Fri, 25 Sep 2009, Moshe Bar wrote: > > > > > or of the parahippocampal cortex? > > > > On Sep 25, 2009, at 10:44 AM, Kelly Silva wrote: > > > >> Hello, > >> Is there any way to calculate the cortical thickness of > perirhinal > >> cortex? > >> Thanks in advance, Kelly > >> > >> Veja quais são os assuntos do momento no Yahoo! + Buscados: Top > 10 - > >> Celebridades - Música - > >> Esportes_______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer September 2009