[Freesurfer] "redraw failed: no gl window open" problem
Hi, there, I am running the tksurfer command to view the cortical surface data as tksurfer bert lh inflated. But I met a problem. I only can view a sliver part of the brain. This sliver portion can rotate and do everything that tksurfer is supposed to do, but I can't view any more of the brain than a tiny piece. Tkmedit works fine. When I run the command, it gave me something like this: surfer: current subjects dir: /home/m047599/freesurfer-install/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599/freesurfer-install/freesurfer surfer: Reading header info from /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I searched the previous posts, it looks like somebody have the same problem. There is no NVidia and native Linux system on my computer. I run tksurfer on a virtual Linux machine using NX 3. 3. 0. 6. I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX. I ran the glxgrears, it works, although very slow. So, how can I solve this problem, any suggestions are highly appreciated. Thanks a lot! Guang _ Get free photo software from Windows Live http://www.windowslive.com/online/photos?ocid=PID23393::T:WLMTAGL:ON:WL:en-US:SI_PH_software:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FW: "redraw failed: no gl window open" problem
Thanks a lot, I have tried this one. It does not work. I knew someone can solve this problem on a local machine by extracting a NVidia driver files and copying it to somewhere to overwrite some original OpenGL files. But I do not want to do this procedure on each computer in our labs. From: p...@netfilter.com.br Date: Wed, 5 Aug 2009 11:21:43 -0300 Subject: Re: [Freesurfer] "redraw failed: no gl window open" problem To: freesurfer...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu setenv doublebufferflag=0tksurfer bert lh inflated--- Pedro Paulo de M. Oliveira Junior 2009/8/5 Guang Zeng Hi, there, I am running the tksurfer command to view the cortical surface data as tksurfer bert lh inflated. But I met a problem. I only can view a sliver part of the brain. This sliver portion can rotate and do everything that tksurfer is supposed to do, but I can't view any more of the brain than a tiny piece. Tkmedit works fine. When I run the command, it gave me something like this: surfer: current subjects dir: /home/m047599/freesurfer-install/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599/freesurfer-install/freesurfer surfer: Reading header info from /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I searched the previous posts, it looks like somebody have the same problem. There is no NVidia and native Linux system on my computer. I run tksurfer on a virtual Linux machine using NX 3. 3. 0. 6. I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX. I ran the glxgrears, it works, although very slow. So, how can I solve this problem, any suggestions are highly appreciated. Thanks a lot! Guang Get free photo software from Windows Live Click here. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Windows Live™: Keep your life in sync. Check it out. _ Express your personality in color! Preview and select themes for Hotmail®. http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_express:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display
Maybe you can try to update your graphic card driver > Date: Wed, 5 Aug 2009 18:24:44 +0100 > From: jerome.sal...@psy.ox.ac.uk > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] tksurfer display > > Help, > Sorry to bother you, but I am looking for my > tksurfer hero! I just installed freesurfer on my laptop (centos5 > virtual machine, 4Go RAM, NIVDIA quadro 110M, intel duo t2...@1.66ghz). > Everything goes well until I tried tksurfer. Only the anterior part of > bert's brain is displayed.(medit is ok; refreshing the > tksurfer view doesn't change the display). > Is there a way to fix my > problem or is my graphic card not performant enough ? > Thanks a lot for your help > Cheers, > J > > -- > __ > Jerome SALLET > > Decision and Action Laboratory > > Department of Experimental Psychology, > University of Oxford > > South Parks Road, OX1 3UD,UK > > Tel (office): (0044) 1865 271 315 > Tel (elsewhere) : (0044) 7 530 060 839 > > > http://psyweb.psy.ox.ac.uk/rushworth/default.htm > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Express your personality in color! Preview and select themes for Hotmail®. http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_express:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert question
Hi, there, I am new to FreeSurfer, just got a question about the mri_convert command. I have a 169x256x256 binary volume, the format is .nii. I called the mri_convert command to convert it to .mgz format. I open the .mgz volume using tkmedit, and then open the .nii volume using fsl view, I got to a problem, I input the same volume index in tkmedit and fsl view, I got the two different views. I think that is because mri_convert will automatically convert the input volume to a 256x256x256 volume, am I right? If I am right, how can I convert the 256x256x256 volume to the original size when I call mri_convert again to convert the .mgz back to .nii. Thanks a lot! Guang _ Windows Live™: Keep your life in sync. http://windowslive.com/explore?ocid=PID23384::T:WLMTAGL:ON:WL:en-US:NF_BR_sync:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert question
Hi, Doug, Thanks a lot, at first I think it may because I use recon-all command which will call mri_convert .. --conform at the motion correction step. I did a simple test, I ran mri_convert A.nii test_data2_orig.mgz, it gave ne something like, $ mri_convert A.nii test_data2_orig.mgz mri_convert A.nii test_data2_orig.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from A.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.993271, 0.0255268, 0.112962) j_ras = (0.00635944, 0.961911, -0.273288) k_ras = (-0.115635, 0.272168, 0.955276) writing to test_data2_orig.mgz... I opened A.nii using fsl view and test_data2_orig.mgz using tkmedit, I input the same volume index and I got the two different views. Is it because of i_ras, j_ras and k_ras? Sorry, I am new to FreeSurfer. Your help are highly appreciated! Guang > Date: Fri, 7 Aug 2009 18:31:56 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert question > > Guang, > > mri_convert does NOT automatically convert to 256^3, but it will with > the -conform option. I have to have your command line to tell for sure. > This is why you should ALWAYS include a command line with your post. In > fact, you should see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for > all the things that will make it easy for us to help you. > > thanks! > > doug > > Guang Zeng wrote: > > Hi, there, > > > > I am new to FreeSurfer, just got a question about the mri_convert command. > > I have a 169x256x256 binary volume, the format is .nii. > > I called the mri_convert command to convert it to .mgz format. > > I open the .mgz volume using tkmedit, and then open the .nii volume > > using fsl view, > > I got to a problem, I input the same volume index in tkmedit and fsl > > view, I got the > > two different views. > > > > I think that is because mri_convert will automatically convert the > > input volume to a 256x256x256 volume, am I right? > > If I am right, how can I convert the 256x256x256 volume to the > > original size when I call mri_convert again to convert the .mgz back > > to .nii. > > > > Thanks a lot! > > > > Guang > > > > > > Windows Live™: Keep your life in sync. Check it out. > > <http://windowslive.com/explore?ocid=PID23384::T:WLMTAGL:ON:WL:en-US:NF_BR_sync:082009> > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Express your personality in color! Preview and select themes for Hotmail®. http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_express:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_normalize problem
Hi, there, I have a question about the mri_normalize command, I do not want to use conform, so my command line is mri_normalize -g 1 -noconform nu.mgz T1.mgz I got an error message as: using max gradient = 1.000 performing kinder gentler normalization... not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform -1.241 0.006 0.133 1.851; 0.087 0.889 0.292 1.071; 0.125 -0.275 0.973 -6.721; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 MRInormGentlyFindControlPoints: unsupported src format 3 MRI3dGentleNormalize failure! mri_ctrl=NULL Does this mean that I must load a control data? Is there a way that I can use the mri_normalzie command without conform and control data? Thanks a lot! Guang _ Get free photo software from Windows Live http://www.windowslive.com/online/photos?ocid=PID23393::T:WLMTAGL:ON:WL:en-US:SI_PH_software:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_normalize problem
Hi, Bruce, Thanks, I tried -no1d, it does not work. I think now my question is once the original volume is conformed to 256x256x256, and we ran the recon-all command to get the surface data. Is there a way I can use mri_convert the volume back to the original size? Thanks a lot! Guang > Date: Sat, 8 Aug 2009 13:24:11 -0400 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_normalize problem > > Hi Guang, > > try using it with -no1d. This will skip the stuff that is trying to fit the > bias field with a spline. Not sure if it will work in general though, we > almost never use it without conforming. > > cheers, > Bruce > > > On Sat, 8 Aug 2009, Guang Zeng wrote: > > > > > Hi, there, > > > > I have a question about the mri_normalize command, I do not want to use > > conform, so > > my command line is mri_normalize -g 1 -noconform nu.mgz T1.mgz > > > > I got an error message as: > > > > using max gradient = 1.000 > > performing kinder gentler normalization... > > not interpolating and embedding volume to be 256^3... > > reading from nu.mgz... > > normalizing image... > > talairach transform > > -1.241 0.006 0.133 1.851; > > 0.087 0.889 0.292 1.071; > > 0.125 -0.275 0.973 -6.721; > > 0.000 0.000 0.000 1.000; > > INFO: Modifying talairach volume c_(r,a,s) based on average_305 > > MRIsplineNormalize(): npeaks = 3 > > Starting OpenSpline(): npoints = 3 > > MRInormGentlyFindControlPoints: unsupported src format 3 > > MRI3dGentleNormalize failure! mri_ctrl=NULL > > > > Does this mean that I must load a control data? > > Is there a way that I can use the mri_normalzie command without conform and > > control data? > > > > Thanks a lot! > > > > Guang > > > > > > _ > > Get free photo software from Windows Live > > http://www.windowslive.com/online/photos?ocid=PID23393::T:WLMTAGL:ON:WL:en-US:SI_PH_software:082009 _ Windows Live™: Keep your life in sync. http://windowslive.com/explore?ocid=PID23384::T:WLMTAGL:ON:WL:en-US:NF_BR_sync:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] question about talairach transform used in skullstrip
Hi, there, In the skullstrip step, mri_em_register command is called and a talairach_with_skull.lta file is produced. This lta file will be used in the following mri_watershed command. My questions are: (1) Once we got the brainmask.auto.mgz, which command we can use to inverse the talairach transform, convert the coordinate to the original system? (2) How different it will be if no altas is used in the mri_watershed step? Thanks a lot! Guang _ Get back to school stuff for them and cashback for you. http://www.bing.com/cashback?form=MSHYCB&publ=WLHMTAG&crea=TEXT_MSHYCB_BackToSchool_Cashback_BTSCashback_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a "redraw failed: no gl window open" problem
Hi, there, I am still facing the problem of "redraw failed: no gl window open", I got another linux machine with Nvidia graphic card, I ran the tksurfer command "tksurfer bert lh inflated", it still gave me the "redraw failed: no gl window open" error. surfer: current subjects dir: /home/m047599/freesurfer-install/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599 surfer: Reading header info from /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: double buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I read a previously posted thread by Nick, it looks like we can download a new tksurfer.bin file to solve this problem at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64But I clicked the link, the file has been removed. Does any one can help me get the new link of this file? Thanks a lot! Guang _ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] a "redraw failed: no gl window open" problem
yeah, it didn't work From: p...@netfilter.com.br Date: Tue, 18 Aug 2009 19:46:02 -0300 Subject: Re: [Freesurfer] a "redraw failed: no gl window open" problem To: freesurfer...@hotmail.com I suppose you have tried the trick bellow setenv doublebuffer_flag 1--- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- New Netfilter Small Business 2009/8/18 Guang Zeng Hi, there, I am still facing the problem of "redraw failed: no gl window open", I got another linux machine with Nvidia graphic card, I ran the tksurfer command "tksurfer bert lh inflated", it still gave me the "redraw failed: no gl window open" error. surfer: current subjects dir: /home/m047599/freesurfer-install/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599 surfer: Reading header info from /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: double buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I read a previously posted thread by Nick, it looks like we can download a new tksurfer.bin file to solve this problem at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64 But I clicked the link, the file has been removed. Does any one can help me get the new link of this file? Thanks a lot! Guang Windows Live: Keep your friends up to date with what you do online. Find out more. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_faster:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] a "redraw failed: no gl window open" problem
Hello, Nick, The freesurfer I am using now is freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full.tar.gz Yes, the glxgears work well. Guang > Subject: Re: [Freesurfer] a "redraw failed: no gl window open" problem > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Date: Tue, 18 Aug 2009 19:27:11 -0400 > > Guang, > > which version of freesurfer are you running? > > does glxgears work? > > can you send me your /etc/X11/xorg.conf file? > > Nick > > > On Tue, 2009-08-18 at 17:53 -0500, Guang Zeng wrote: > > yeah, it didn't work > > > > > > __ > > From: p...@netfilter.com.br > > Date: Tue, 18 Aug 2009 19:46:02 -0300 > > Subject: Re: [Freesurfer] a "redraw failed: no gl window open" problem > > To: freesurfer...@hotmail.com > > > > I suppose you have tried the trick bellow > > > > setenv doublebuffer_flag 1 > > --- > > Pedro Paulo de M. Oliveira Junior > > Diretor de Operações > > Netfilter & SpeedComm Telecom > > --- Novo Netfilter 3.0 www.Netfilter.com.br > > --- New Netfilter Small Business > > > > > > > > 2009/8/18 Guang Zeng > > Hi, there, > > > > I am still facing the problem of "redraw failed: no gl window > > open", I got another linux machine with Nvidia graphic card, > > I ran the tksurfer command "tksurfer bert lh inflated", it > > still gave me the "redraw failed: no gl window open" error. > > > > surfer: current subjects > > dir: /home/m047599/freesurfer-install/freesurfer/subjects > > surfer: not in "scripts" dir ==> using cwd for session root > > surfer: session root data dir ($session) set to: > > surfer: /home/m047599 > > surfer: Reading header info > > from > > /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz > > surfer: vertices=131369, faces=262734 > > Loading > > /home/m047599/freesurfer-install/freesurfer/surface_labels.txt > > surfer: ### redraw failed: no gl window open > > surfer: double buffered window > > surfer: tkoInitWindow(bert) > > surfer: using > > interface > > /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl > > Reading > > /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl > > Reading > > /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl > > Reading > > /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl > > Reading > > /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl > > Successfully parsed tksurfer.tcl > > reading white matter vertex locations... > > > > I read a previously posted thread by Nick, it looks like we > > can download a new tksurfer.bin file to solve this problem at > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64 > > But I clicked the link, the file has been removed. Does any > > one can help me get the new link of this file? > > > > Thanks a lot! > > > > Guang > > > > > > > > __ > > Windows Live: Keep your friends up to date with what you do > > online. Find out more. > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > __ > > Hotmail® is up to 70% faster. Now good news travels really fast. Try > > it now. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] a "redraw failed: no gl window open" problem
Hi, Nick, I forgot to attach the xorg.cong file, it is here. Thanks! # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 1.0 (buildmeis...@builder26) Wed Mar 29 15:31:59 PST 2006 # Xorg configuration created by system-config-display Section "ServerLayout" Identifier "Default Layout" Screen 0 "Screen0" 0 0 InputDevice"Mouse0" "CorePointer" InputDevice"Keyboard0" "CoreKeyboard" EndSection Section "Files" # RgbPath is the location of the RGB database. Note, this is the name of the # file minus the extension (like ".txt" or ".db"). There is normally # no need to change the default. # Multiple FontPath entries are allowed (they are concatenated together) # By default, Red Hat 6.0 and later now use a font server independent of # the X server to render fonts. RgbPath "/usr/X11R6/lib/X11/rgb" FontPath "unix/:7100" EndSection Section "Module" Load "dbe" Load "extmod" Load "fbdevhw" Load "glx" Load "record" Load "freetype" Load "type1" Load "dri" EndSection Section "ServerFlags" Option"AllowMouseOpenFail" "yes" EndSection Section "InputDevice" # Specify which keyboard LEDs can be user-controlled (eg, with xset(1)) #Option"Xleds""1 2 3" # To disable the XKEYBOARD extension, uncomment XkbDisable. #Option"XkbDisable" # To customise the XKB settings to suit your keyboard, modify the # lines below (which are the defaults). For example, for a non-U.S. # keyboard, you will probably want to use: #Option"XkbModel""pc102" # If you have a US Microsoft Natural keyboard, you can use: #Option"XkbModel""microsoft" # # Then to change the language, change the Layout setting. # For example, a german layout can be obtained with: #Option"XkbLayout""de" # or: #Option"XkbLayout""de" #Option"XkbVariant""nodeadkeys" # # If you'd like to switch the positions of your capslock and # control keys, use: #Option"XkbOptions""ctrl:swapcaps" # Or if you just want both to be control, use: #Option"XkbOptions""ctrl:nocaps" # Identifier "Keyboard0" Driver "kbd" Option"XkbModel" "pc105" Option"XkbLayout" "us" EndSection Section "InputDevice" Identifier "Mouse0" Driver "mouse" Option"Protocol" "IMPS/2" Option"Device" "/dev/input/mice" Option"ZAxisMapping" "4 5" Option"Emulate3Buttons" "no" EndSection Section "Monitor" Identifier "Monitor0" VendorName "Monitor Vendor" ModelName"Unknown monitor" HorizSync31.0 - 54.0 VertRefresh 50.0 - 120.0 Option"dpms" EndSection Section "Device" Identifier "Videocard0" Driver "nvidia" VendorName "Videocard vendor" BoardName "NVIDIA Quadro FX 4400" EndSection Section "Screen" Identifier "Screen0" Device "Videocard0" Monitor"Monitor0" DefaultDepth 24 Option"NvAGP" "1" Option"TwinView" "true" Option"SecondMonitorHorizSync" "31.0 - 80.0" Option"SecondMonitorVertRefresh" "56.0 - 76.0" Option"MetaModes" "1600x1200, 1600x1200; 1280x1024, 1280x1024; 1280x1024, 1280x1024;" Option"TwinViewOrientation" "RightOf" Option"Xinerama" "on" SubSection "Display" Viewport 0 0 Depth 16 Modes"1024x768" "800x600" "640x480" EndSubSection SubSection "Display" Viewport 0 0 Depth 24 Modes"1024x768" "800x600" "640x480" EndSubSection EndSection > Subject: Re: [Freesurfer] a "redraw failed: no gl window open" problem > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Date: Tue, 18 Aug 2009 19:27:11 -0400 > > Guang, > > which version of freesurfer are you running? > > does glxgear
[Freesurfer] tkregsiter2 problem
Hi, there, I have the two scans (001.mgz and 002.mgz) of the same subject, 001.mgz is used as the input of recon-all -autorecon1, now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz using brainmask.mgz as reference volume, which command I can use? tkregister2? Thanks a lot! Guang _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_faster:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregsiter2 problem
Hi, Greve, Thanks a lot! It works. But I got another question now, I used mri_convert to convert a NIFTI file 002.nii to MGZ file 002.mgz. I also want to register 002.nii using the brainmask as the reference volume. Here, 002.nii is a 180x256x256 volume. My command line is bbregister --s data_2 --mov 002.nii --init-fsl --t1 --reg nureg.dat --o nuDReg.mgz There is no error when the program is running, however the registration results is bad. Could you give some suggestions? Guang > Date: Wed, 19 Aug 2009 16:59:11 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] tkregsiter2 problem > > Use bbregister, something like: > > bbregister --s subjectname --mov 002.mgz --init-fsl --t1 --reg > register.dat --o 002.anat.mgz > > > > Guang Zeng wrote: > > Hi, there, > > > > I have the two scans (001.mgz and 002.mgz) of the same subject, > > 001.mgz is used as the input of recon-all -autorecon1, > > now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz > > using brainmask.mgz as reference volume, which command I can use? > > tkregister2? > > > > Thanks a lot! > > Guang > > > > > > Hotmail® is up to 70% faster. Now good news travels really fast. Try > > it now. > > <http://windowslive.com/online/hotmail?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_faster:082009> > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > _ Get back to school stuff for them and cashback for you. http://www.bing.com/cashback?form=MSHYCB&publ=WLHMTAG&crea=TEXT_MSHYCB_BackToSchool_Cashback_BTSCashback_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregsiter2 problem
Hello, Dr. Greve, I used the vol2vol command with the previously acquired reg.dat, It looks ok now. Thanks! Guang > Date: Wed, 19 Aug 2009 16:59:11 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] tkregsiter2 problem > > Use bbregister, something like: > > bbregister --s subjectname --mov 002.mgz --init-fsl --t1 --reg > register.dat --o 002.anat.mgz > > > > Guang Zeng wrote: > > Hi, there, > > > > I have the two scans (001.mgz and 002.mgz) of the same subject, > > 001.mgz is used as the input of recon-all -autorecon1, > > now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz > > using brainmask.mgz as reference volume, which command I can use? > > tkregister2? > > > > Thanks a lot! > > Guang > > > > > > Hotmail® is up to 70% faster. Now good news travels really fast. Try > > it now. > > <http://windowslive.com/online/hotmail?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_faster:082009> > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > _ Get back to school stuff for them and cashback for you. http://www.bing.com/cashback?form=MSHYCB&publ=WLHMTAG&crea=TEXT_MSHYCB_BackToSchool_Cashback_BTSCashback_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] bbregister question
Hi, there, Sorry, I asked the same question yesterday, but I think I didn't explain it clear. I have the two scans (001.mgz and 002.mgz) of the same subject, 001.mgz is used as the input of recon-all -autorecon1, and I only run -autorecon1. now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz using brainmask.mgz as reference volume. Dr. Greve mentioned that I can use bbregister, but I got a problem now, becuase I only run autorecon1, I do not have lh.white which will be acquired after autorecon2. The bbregister command stopped in the middel. My command line is bbregister --s data_2 --mov 002.mgz --init-fsl --t1 --reg brainreg.dat --o brainmaskReg.mgz I got a error as, Loading mov Loading lh.white surf No such file or directory Is there an option that I do not use lh.white, just use the information I got after autorecon1 to do the registration, or I need use other commands? Thanks a lot! Guang _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_facebook:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about mri_convert
Hi, there, I got a question about mri_convert. I have a brainmask.nii file, (max intensity value is 64, and minimum intensity is 0), it shows good intensity contrast. Now I want to use mri_convert to convert it to mgz file, my command line is mri_convert A.nii --conform A.mgz Now, I open A.mgz using Tkmedit, I can not see those significant intensity contrast now, and the max intensity value is 255, and minimum intensity is 0 It looks like mri_convert do something like histogram equalization or normalization. Will mri_convert actually change the intensity value of each voxel? Can I keep my original intensity value for each voxel? Use the mri_convert -sc? Thanks a lot! Guang _ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FW: a question about mri_convert
Actually, I also noticed that when mri_convert runs, it says something like "changing data type from 3 to 0 " The data type of the nii file is float32, while the converted .mgz id uchar, is it the problem? Thanks Guang From: freesurfer...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 21 Aug 2009 11:37:18 -0500 Subject: [Freesurfer] a question about mri_convert Hi, there, I got a question about mri_convert. I have a brainmask.nii file, (max intensity value is 64, and minimum intensity is 0), it shows good intensity contrast. Now I want to use mri_convert to convert it to mgz file, my command line is mri_convert A.nii --conform A.mgz Now, I open A.mgz using Tkmedit, I can not see those significant intensity contrast now, and the max intensity value is 255, and minimum intensity is 0 It looks like mri_convert do something like histogram equalization or normalization. Will mri_convert actually change the intensity value of each voxel? Can I keep my original intensity value for each voxel? Use the mri_convert -sc? Thanks a lot! Guang Windows Live: Keep your friends up to date with what you do online. Find out more. _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_facebook:082009___ 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
Re: [Freesurfer] FW: a question about mri_convert
I tried using mri_convert without conform, same thing. Basically, I think if I set -ns = 1 when I use mri_convert, it will not rescale the image. But when I open it using tkmedit, I still can not see the intensity contrast. So I think my question is why the same volume (with the same max intensity and minimum intensity) looks different in fslview and tkmedit? Thanks! Guang > Date: Fri, 21 Aug 2009 13:05:25 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: a question about mri_convert > > why do you want to conform it? > > Guang Zeng wrote: > > Actually, I also noticed that when mri_convert runs, it says something > > like "changing data type from 3 to 0 " > > The data type of the nii file is float32, while the converted .mgz id > > uchar, is it the problem? > > > > > > Thanks > > Guang > > > > > > From: freesurfer...@hotmail.com > > To: freesurfer@nmr.mgh.harvard.edu > > Date: Fri, 21 Aug 2009 11:37:18 -0500 > > Subject: [Freesurfer] a question about mri_convert > > > > Hi, there, > > > > I got a question about mri_convert. > > I have a brainmask.nii file, (max intensity value is 64, and minimum > > intensity is 0), it shows good intensity contrast. > > Now I want to use mri_convert to convert it to mgz file, my command > > line is > > > > mri_convert A.nii --conform A.mgz > > > > Now, I open A.mgz using Tkmedit, I can not see those significant > > intensity contrast now, and the max intensity value is 255, and > > minimum intensity is 0 > > It looks like mri_convert do something like histogram equalization or > > normalization. > > > > Will mri_convert actually change the intensity value of each voxel? > > Can I keep my original intensity value for each voxel? Use the > > mri_convert -sc? > > > > Thanks a lot! > > > > Guang > > > > > > > > Windows Live: Keep your friends up to date with what you do online. > > Find out more. > > <http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009> > > > > Windows Live: Make it easier for your friends to see what you’re up to > > on Facebook. Find out more. > > <http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_facebook:082009> > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Get back to school stuff for them and cashback for you. http://www.bing.com/cashback?form=MSHYCB&publ=WLHMTAG&crea=TEXT_MSHYCB_BackToSchool_Cashback_BTSCashback_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9
Hi, there,
Could you tell me what I need to unpack to solve the "redraw fails" problem?
Thanks a lot!
Guang
> > if I recall correctly "the sliver problem" stems from the use of an
> > incompatible libGL. I did the following that a colleague found out:
> > add the following line to ${FREESURFER_HOME}/bin/tksurfer (that is
> > the script that calls tksurfer.bin):
> > setenv LD_PRELOAD ${FREESURFER_HOME}bin/libGL.so.1
> >
> > Also unpack the following to reside in your ${FREESURFER_HOME}/bin
> > directory:
> >
> >
> >
> >
> > (Those are GL libraries from a redhat 4 / centos 4 system that seem
> > to work with tksurfer).
> From: sebastian.moel...@lur.rwth-aachen.de
> To: corinna...@gmail.com
> Subject: Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9
> Date: Mon, 10 Aug 2009 11:36:21 -0700
> CC: freesurfer@nmr.mgh.harvard.edu; freesurfer...@hotmail.com;
> ni...@nmr.mgh.harvard.edu
>
> Hi,
>
> it seems that my fix is not universal.. Do you see anything at all? In
> my case I use NX remote controlling on red hat enterprise linux server
> with the described fix. NX on 32 bit windows works as does Macosx,
> only Vista 64bit clients running NX to log into the server fail to use
> double buffering (they do display everything in tksurfer though just
> really slow). Hmm, I have no real idea what might be going on there,
> sorry...
>
> Sebastian
>
> On Aug 10, 2009, at 11:06 AM, corinna bauer wrote:
>
> > Hello,
> >
> > I also received the same error message as Guang when trying to run
> > tksurfer. I added the suggested line to $FREESURFER_HOME/bin/
> > tksurfer and unpacked the files, but I still get the following error
> > message:
> >
> > surfer: current subjects dir: /home/freesurfer4.4.0/subjects/corinna/
> > ADNI
> > surfer: not in "scripts" dir ==> using cwd for session root
> > surfer: session root data dir ($session) set to:
> > surfer: /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057
> > surfer: Reading header info from /home/freesurfer4.4.0/subjects/
> > corinna/ADNI/003_S_1057/mri/T1.mgz
> > surfer: vertices=116670, faces=26
> > Loading /home/freesurfer4.4.0/surface_labels.txt
> > surfer: ### redraw failed: no gl window open
> > surfer: single buffered window
> > surfer: tkoInitWindow(003_S_1057)
> > surfer: using interface /home/freesurfer4.4.0/lib/tcl/tksurfer.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/tkm_common.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/tkm_wrappers.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/fsgdfPlot.tcl
> > Reading /home/freesurfer4.4.0/lib/tcl/tkUtils.tcl
> > Successfully parsed tksurfer.tcl
> > reading white matter vertex locations...
> >
> > I also tried setenv doublebufferflag 0, which also did not work.
> >
> > Thanks,
> >
> > Corinna
> >
> > On Wed, Aug 5, 2009 at 1:05 PM, Sebastian Moeller
> > > > wrote:
> > Hi Guang,
> >
> > if I recall correctly "the sliver problem" stems from the use of an
> > incompatible libGL. I did the following that a colleague found out:
> > add the following line to ${FREESURFER_HOME}/bin/tksurfer (that is
> > the script that calls tksurfer.bin):
> > setenv LD_PRELOAD ${FREESURFER_HOME}bin/libGL.so.1
> >
> > Also unpack the following to reside in your ${FREESURFER_HOME}/bin
> > directory:
> >
> >
> >
> >
> > (Those are GL libraries from a redhat 4 / centos 4 system that seem
> > to work with tksurfer).
> >
> >
> > Nick, do you think it would be possible to make this change for the
> > distribution (it was inspired by your inclusion of libGlut to begin
> > with).
> >
> > ahoi & good luck
> >Sebastian
> >
> >
> > On Aug 5, 2009, at 7:22 AM, freesurfer-requ...@nmr.mgh.harvard.edu
> > wrote:
> >
> > Date: Wed, 5 Aug 2009 08:49:15 -0500
> > From: Guang Zeng
> > Subject: [Freesurfer] "redraw failed: no gl window open" problem
> > To:
> > Message-ID:
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> > Hi, there,
> >
> > I am running the tksurfer command to view the cortical surface data
> > as tksurfer bert lh inflated. But I met a problem.
> > I only can view a sliver part of the brain. This sliver portion can
> > rotate and do everything that tksurfer is supposed to do,
> > but I can't view any more of the brain than a tiny piece. Tkmedit
> > works f
[Freesurfer] a question about mri_convert and mri_vol2vol
Hi, there, I used FreeSurfer pipeline to study a subject, I convert my .nii file to .mgz file, and then send it to FreeSurfer pipeline.Everything works well. Now I want to convert the wmparc.mgz back to the space that the original volume was. I tried two command mri_covert wmparc.mgz -rl orig.nii new.nii and mri_vol2vol --mov wmparc.mgz --targ orig.nii --regheader --o new.ii Both of them gave me the same problem. My original volume is : qform_name Aligned Anat qform_code 2 qto_xyz:1 -1.198313 -0.049354 0.044215 94.332878 qto_xyz:2 -0.041108 1.237333 0.172261 -131.942123 qto_xyz:3 0.048546 -0.170504 1.237284 -105.448372 qto_xyz:4 0.00 0.00 0.00 1.00 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Aligned Anat sform_code 2 sto_xyz:1 -1.198313 -0.049354 0.044217 94.332878 sto_xyz:2 -0.041108 1.237333 0.172261 -131.942108 sto_xyz:3 0.048547 -0.170504 1.237284 -105.448372 sto_xyz:4 0.00 0.00 0.00 1.00 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior Now the new resampled volume is: qform_name Scanner Anat qform_code 1 qto_xyz:1 1.198313 -0.049354 0.044217 -96.198837 qto_xyz:2 0.041108 1.237333 0.172261 -138.478333 qto_xyz:3 -0.048547 -0.170504 1.237284 -97.729370 qto_xyz:4 0.00 0.00 0.00 1.00 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Scanner Anat sform_code 1 sto_xyz:1 1.198313 -0.049354 0.044217 -96.198837 sto_xyz:2 0.041108 1.237333 0.172261 -138.478333 sto_xyz:3 -0.048547 -0.170504 1.237284 -97.729370 sto_xyz:4 0.00 0.00 0.00 1.00 sform_xorient Left-to-Right sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior When I use fslview to view these two volumes, their orientations were swapped. Could you help me fix this problems? Thanks a lot! Guang _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_facebook:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] comparison of volume difference
Hi, there, I am wondering how i can do a comparison of two scans of the same object, calculating the percent volume difference and percent volume overlap of hippocampus,...etc. Somebody can give me a hint? Thanks a lot! Guang Zeng _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:WM_HYGN_faster:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampus volume comparision
Hi, there, I converted a subject from nii (160x256x256) to mgz (256 x 256 x 256 ), and then sent it to the FreeSurfer pipeline. Now, I'd like to compare the resulted hippocampus volume with a hand tracing hippocampus using the original volume. What is the best way to do it? I think I can not use the data in the aseg.stats directly, right? Because of the conform. Thanks a lot! Guang Zeng _ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_volmask description
Hello, there, Do you know where I can find a description for mris_volmask. The page on FreeSurferWiki about this is empty. Thanks a lot! Zeng _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_facebook:082009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] longitudinal study
Hi, there, I am going to run the FreeSurfer Longitudinal Stream (FS 4.5) on data from different timepoints. Do we need cross-sectionally process all time points with the default workflow, or just need run the first step of the default workflow. Thanks a lot! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/171222986/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to extract segmented hippocampus
Hi, there, I'd like to extract the left and right hippocampus from aseg.mgz, so basically what I want is a volume where left hippocampus have value (or label) 17 and right hippocampus have value (or label) 53, all the other place are zero. How can I do it? Using mri_threshold or mri_label2vol? Thanks a lot! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampus volume are different after step.3
Hi, there, I ran a subject through FreeSurfer pipeline. I found that the size of left and right hippocampus in aseg.stats are larger than that of left and right hippocampus in wmparc.stats after step. 3. If I want to compare the FreeSurfer segmented hippocampus with a manually traced hippocampus, which value I should use, the result from step.2 or step. 3? Thanks a lot! Guang _ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkregister2 question
Hi, there, I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction cosine info. So everytime when I try to register another nifti file case_2.nii to it using tkregister2 or mri_vol2vol, it always complains that "INFO: could not find ../../case_1.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ../../case_1.mat file" Just want to know if there are other methods I can use to register case_1 and case_2? Any kinds of method! Thanks a lot! Guang _ Bing™ brings you maps, menus, and reviews organized in one place. Try it now. http://www.bing.com/search?q=restaurants&form=MLOGEN&publ=WLHMTAG&crea=TEXT_MLOGEN_Core_tagline_local_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2 question
Hello, Nick, Thanks a lot for your help. The bad thing is case_1&2 are not oriented the same way. Anything else I can do? Guang > Subject: Re: [Freesurfer] tkregister2 question > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Date: Sat, 19 Sep 2009 11:51:28 -0400 > > Guang, > > If you're 100% certain that case_2 is oriented the same way as case_1, > for instance if they were from the same scanner, then you can do this: > > mri_convert case_2.nii case_2.img > > (this outputs case_2.mat) > > cp case_2.mat case_1.mat > > now tkregister2 should work. Keep in mind this is a hack accounting for > the missing case_1 data. If the data is from different scanners, then > there is a risk of L-R reversal, because the orientation info may not be > the same. > > Nick > > > On Fri, 2009-09-18 at 17:33 -0500, Guang Zeng wrote: > > Hi, there, > > > > I have a case_1.hdr file and case_1.img file, but no the > > corresponding .mat file which contains the necessary direction cosine > > info. > > So everytime when I try to register another nifti file case_2.nii to > > it using tkregister2 or mri_vol2vol, it always complains that > > > > "INFO: could not find ../../case_1.mat file for direction cosine info. > > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped > > (default). > > INFO: if not valid, please provide the information in ../../case_1.mat > > file" > > > > Just want to know if there are other methods I can use to register > > case_1 and case_2? Any kinds of method! > > > > Thanks a lot! > > > > Guang > > > > > > > > __ > > Bing™ brings you maps, menus, and reviews organized in one place. Try > > it now. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2 question
Hello, Nick, Which version of orient_mri you are using? I read this from FreeSurfer Wiki "First, load up a volume either by passing one on the command line or by using the File menu command or toolbar button. You will see the volume in four views." However when I call orient_mri, I only saw one view, not four. My version of orient_mri is 1.0. Thanks a lot! Guang > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Date: Mon, 21 Sep 2009 10:58:15 -0400 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] tkregister2 question > > Guang, > > You could use the freesurfer utility 'orient_mri'. > > First open case_1: > > orient_mri --volume case_1.img > > then case_2: > > orient_mri --volume case_2.nii > > Then use the rotate icons to rotate case_1 so that its oriented the same > as case_2, and save the case_1 volume (you can save as 'case_1.nii'). > Then you can use tkregister2. > > Again, without fudicial markers, its difficult to tell left from right, > so there is no guarantee that your l-r orientation is correct. > > Nick > > > > On Sun, 2009-09-20 at 12:31 -0500, Guang Zeng wrote: > > > > Hello, Nick, > > > > Thanks a lot for your help. The bad thing is case_1&2 are not oriented > > the same way. > > Anything else I can do? > > > > > > > > > > Guang > > > > > Subject: Re: [Freesurfer] tkregister2 question > > > From: ni...@nmr.mgh.harvard.edu > > > To: freesurfer...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Date: Sat, 19 Sep 2009 11:51:28 -0400 > > > > > > Guang, > > > > > > If you're 100% certain that case_2 is oriented the same way as > > case_1, > > > for instance if they were from the same scanner, then you can do > > this: > > > > > > mri_convert case_2.nii case_2.img > > > > > > (this outputs case_2.mat) > > > > > > cp case_2.mat case_1.mat > > > > > > now tkregister2 should work. Keep in mind this is a hack accounting > > for > > > the missing case_1 data. If the data is from different scanners, > > then > > > there is a risk of L-R reversal, because the orientation info may > > not be > > > the same. > > > > > > Nick > > > > > > > > > On Fri, 2009-09-18 at 17:33 -0500, Guang Zeng wrote: > > > > Hi, there, > > > > > > > > I have a case_1.hdr file and case_1.img file, but no the > > > > corresponding .mat file which contains the necessary direction > > cosine > > > > info. > > > > So everytime when I try to register another nifti file case_2.nii > > to > > > > it using tkregister2 or mri_vol2vol, it always complains that > > > > > > > > "INFO: could not find ../../case_1.mat file for direction cosine > > info. > > > > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > > unflipped > > > > (default). > > > > INFO: if not valid, please provide the information > > in ../../case_1.mat > > > > file" > > > > > > > > Just want to know if there are other methods I can use to register > > > > case_1 and case_2? Any kinds of method! > > > > > > > > Thanks a lot! > > > > > > > > Guang > > > > > > > > > > > > > > > > > > __ > > > > Bing™ brings you maps, menus, and reviews organized in one place. > > Try > > > > it now. > > > > ___ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > __ > > Lauren found her dream laptop. Find the PC that’s right for you. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Microsoft brings you a new way to search the web. Try Bing™ now http://www.bing.com?form=MFEHPG&publ=WLHMTAG&crea=TEXT_MFEHPG_Core_tagline_try bing_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to extract segmented hippocampus
I loaded the left and right hippocampus mesh using tksurfer, it works, Thanks! If I want to paint left hippocampus as yellow and right hippocampus as green after I load them using tksurfer, how could I do it? Thanks! Guang > Date: Thu, 17 Sep 2009 07:24:11 -0400 > From: fis...@nmr.mgh.harvard.edu > To: gro...@computer.org > CC: freesurfer@nmr.mgh.harvard.edu; gr...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to extract segmented hippocampus > > you can use mri_tessellate to create a mesh, then tksurfer will visualize > it > On Thu, 17 Sep 2009, Gonzalo Rojas Costa wrote: > > > Dear Douglas: > > > > And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz > > with the mri_binarize command ?... > > > > Sincerely, > > > > > > Gonzalo Rojas Costa > > > > > >> mri_binarize with --match 17 or --match 53 will do it > >> > >> doug > >> > >> Guang Zeng wrote: > >>> Hi, there, > >>> > >>> I'd like to extract the left and right hippocampus from aseg.mgz, so > >>> basically what I want is a volume where left hippocampus have value > >>> (or label) 17 and right hippocampus have value (or label) 53, all the > >>> other place are zero. > >>> > >>> How can I do it? Using mri_threshold or mri_label2vol? > >>> > >>> Thanks a lot! > >>> > >>> Guang > >>> > >>> > >>> > >>> > >>> Hotmail: Free, trusted and rich email service. Get it now. > >>> <http://clk.atdmt.com/GBL/go/171222984/direct/01/> > >>> > >>> > >>> ___ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> In order to help us help you, please follow the steps in: > >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > ___ > > 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 _ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to use mri_compute_seg_overlap
Hi, there, I have two subjects from two time points, I'd like to compare their overlap ratio of FreeSurfer segmented hippocampus. I try to use the command mri_compute_seg_overlap to do it, My command line is: mri_compute_seg_overlap -olog text tp1/mri/aseg.mgz tp2/mri/aseg.mgz Is it correct? I ran it, but nothing happen. Thanks! Guang _ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to use mri_compute_seg_overlap
Hello, Nick, Yes, I can get the results now, I set the wrong path. Just want to double check, I have send the two subjects (from different time points) to the FreeSurfer longitudinal stream, so the resulted two aseg.mgz files have been registered to the base-template, right? Thanks a lot! Guang > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Date: Wed, 23 Sep 2009 13:01:52 -0400 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to use mri_compute_seg_overlap > > Guang, > > So you did not get output that looked like this? > > logging overall Dice to text > Jaccard Coefficients: > correct ratio for label 2 = 1 > correct ratio for label 41 = 1 > . > . > correct ratio for label 44 = 1 > mean +/- std = 1. +/- 0. > Dice Coefficients: > label 2 = 1 > label 41 = 1 > . > . > . > label 44 = 1 > mean +/- std = 1. +/- 0. > Overall subcortical dice = 1. > > (in this example, i compared the same aseg, so dice will be 1). > > also, make sure your second time point aseg is registered to the first. > if it is not, the your dices will be low, because its just comparing > voxel to voxel. > > Nick > > > On Wed, 2009-09-23 at 11:30 -0500, Guang Zeng wrote: > > Hi, there, > > > > I have two subjects from two time points, I'd like to compare their > > overlap ratio of FreeSurfer segmented hippocampus. > > I try to use the command mri_compute_seg_overlap to do it, > > > > My command line is: > > mri_compute_seg_overlap -olog text tp1/mri/aseg.mgz tp2/mri/aseg.mgz > > > > Is it correct? I ran it, but nothing happen. > > > > Thanks! > > > > Guang > > > > > > > > __ > > Insert movie times and more without leaving Hotmail®. See how. > > ___ > > 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 _ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to use mri_compute_seg_overlap
I think I still need register the second tp aseg.mgz to the first tp aseg.mgz, even they are longitudinal-stream analyzed. The dice coefficients are higher after registration. From: freesurfer...@hotmail.com To: ni...@nmr.mgh.harvard.edu Date: Wed, 23 Sep 2009 13:04:59 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to use mri_compute_seg_overlap Hello, Nick, Yes, I can get the results now, I set the wrong path. Just want to double check, I have send the two subjects (from different time points) to the FreeSurfer longitudinal stream, so the resulted two aseg.mgz files have been registered to the base-template, right? Thanks a lot! Guang > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Date: Wed, 23 Sep 2009 13:01:52 -0400 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to use mri_compute_seg_overlap > > Guang, > > So you did not get output that looked like this? > > logging overall Dice to text > Jaccard Coefficients: > correct ratio for label 2 = 1 > correct ratio for label 41 = 1 > . > . > correct ratio for label 44 = 1 > mean +/- std = 1. +/- 0. > Dice Coefficients: > label 2 = 1 > label 41 = 1 > . > . > . > label 44 = 1 > mean +/- std = 1. +/- 0. > Overall subcortical dice = 1. > > (in this example, i compared the same aseg, so dice will be 1). > > also, make sure your second time point aseg is registered to the first. > if it is not, the your dices will be low, because its just comparing > voxel to voxel. > > Nick > > > On Wed, 2009-09-23 at 11:30 -0500, Guang Zeng wrote: > > Hi, there, > > > > I have two subjects from two time points, I'd like to compare their > > overlap ratio of FreeSurfer segmented hippocampus. > > I try to use the command mri_compute_seg_overlap to do it, > > > > My command line is: > > mri_compute_seg_overlap -olog text tp1/mri/aseg.mgz tp2/mri/aseg.mgz > > > > Is it correct? I ran it, but nothing happen. > > > > Thanks! > > > > Guang > > > > > > > > __ > > Insert movie times and more without leaving Hotmail®. See how. > > ___ > > 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 Insert movie times and more without leaving Hotmail®. See how. _ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to use mri_surf2surf
Hi, there, mri_surf2surf resamples one CorticalSurface onto another. If I have two subjects from different time points (tp1 and tp2), I'd like to compare the FreeSurfer analyzed surface data. For example, could I use mri_surf2surf to resample the white matter surface of tp1 onto tp2, so I can overlay the white matter surface of tp2 to tp1 using tkmedit? Thanks! guang _ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampus volume difference
Hi, there, I use the following matlab code to find right and left hippocampus in aseg.mgz %% filename = 'case_1/mri/aseg.mgz'; [vol, M, mr_parms, volsz] = load_mgh(filename); hippo_left = find( (vol > 16.99) & (vol < 17.01) ); hippo_right = find( (vol > 52.99) & (vol < 53.01) ); %%% I found size(hippo_left, 1) = 3075; size(hippo_right, 1) = 3237; However, the value I found in aseg.mgz is 3162 3162.0 Left-Hippocampus 3390 3390.0 Right-Hippocampus Why these values are different (3075 < 3162, 3237 < 3390)? Thanks a lot! Guang _ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutorial_Storage_062009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?h.aparc.a2005s.stats and ?h.aparc.a2009s.stats
Hi, there, What is the difference between ?h.aparc.a2005s.stats (from ver 4.4) and ?h.aparc.a2009s.stats (from ver 4.5) in the stats folder? ?h.aparc.a2009s.stats is still based on Christophe's atlas, right? Thanks a lot! Guang _ Microsoft brings you a new way to search the web. Try Bing™ now http://www.bing.com?form=MFEHPG&publ=WLHMTAG&crea=TEXT_MFEHPG_Core_tagline_try bing_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] volume difference in aparc.stats and wmparc.stats
Hi, there, I am looking at the volume size of front pole . In lh.aparc.stats, this volume is 590, while in wmparc.stats (it is called ctx-lh-frontalpole), this value is 610, which one is accurate? Thanks a lot! BTW: In FreeSurfer Tutorial : Process Flow (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) The follwing command is called at the end of recon-all -autorecon2 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 006_S_0547_20070924 --surf-wm-vol --ctab /home/m047599/freesurfer-install/freesurfer/ASegStatsLUT.txt However, when I looked at the recon-all.log file, it is called at the very end of autorecon3, am I right? Guang _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141664/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about mri_label_volume -eTIV
Hi, there, >From FS Wiki, eTIV - estimated Total Intracranial Volume, aka ICV, I read mri_label_volume requires specifying the transform file to use, and the scale factor: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53where $sdir is the path to the subject's mri directory (ie, $SUBJECTS_DIR//mri). The '17' and '53' are label ID's, in this case left and right hippocampus (see the subjects /stats/aseg.stats file for IDs). The output will look like: using eTIV from atlas transform of 1528 cm^3 processing label 17... 3822 voxels (3822.0 mm^3) in label 17, %0.250119 of eTIV volume (1528075) processing label 53... 4410 voxels (4410.0 mm^3) in label 53, %0.288598 of eTIV volume (1528075)>From a previous post at FS mailing list, I also read something similar, Just as an aside, once you have a talairach_with_skull.lta file (whether from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), where the scale_factor employed is 2150. Just want to know where dose this scale factor number 1948 and 2150 come from? Thanks a lot! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TIV corrected
Hi, there, Have those volume of ROIs in aseg.stats been TIV corrected? Thanks a lot! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TIV corrected
Hello, Dr. Greve, Is there a method to calculate the TIV corrected volume of ROIs using FS. Thanks a lot! Guang > Date: Tue, 20 Oct 2009 13:04:44 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TIV corrected > > no. > > douig > > Guang Zeng wrote: > > Hi, there, > > > > Have those volume of ROIs in aseg.stats been TIV corrected? > > > > > > > > > > Thanks a lot! > > > > Guang > > > > > > Hotmail: Free, trusted and rich email service. Get it now. > > <http://clk.atdmt.com/GBL/go/171222984/direct/01/> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
Hi, there, I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab? Is it possible to replace FS Atlas with our own Atlas and use it for analysis? Thanks a lot! Guang _ New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID24727::T:WLMTAGL:ON:WL:en-US:WWL_WIN_pcscout:102009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] creat own template
Hi, there, I have two questions, 1. I have read "The surface registration and templates" at FreeSurfer WIKI, and I am going to creat our own registration template. Is there a shell script available somewhere to do this? 2. What are the files in the folder of ../freesurfer/subjects/fsaverage. Are they the results of crosse-sectional FS anlysis using the average of Buckner40 as input. Why there is no wmparc.mgz in /mri Thannks a lot! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_make_template question
Hi, there,
I am going to make our own template. Based on the introduction in FreeSurfer
WIKI "The Surface Registration Process; Template", the first step is "Prep".
"The process starts ("Prep") by choosing one reference subject, and
producing a template (Here, mytemp0.tif). No ?h.sphere is required --
this step uses the subject's own pattern as the reference."
Here, I listed my script for this "Prep" step please let me if it is correct:
mris_make_template lh smoothwm sample_0 my_template0.tif
mris_make_template lh sulc sample_0 my_template0.tif
mris_make_template lh curv sample_0 my_template0.tif
mris_make_template rh smoothwm sample_0 my_template0.tif
mris_make_template rh sulc sample_0 my_template0.tif
mris_make_template rh curv sample_0 my_template0.tif
Thanks a lot!
Guang
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Re: [Freesurfer] mris_make_template question
Hello, Bruce,
Thanks a lot for your help!
I ran 4 commands, and results are shown below:
1.
%%%
mris_make_template lh smoothwm 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1)
reading spherical surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm...
curvature mean = 0.000, std = 1.000
computing parameterization for surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H...
curvature mean = -0.000, std = 0.602
computing parameterization for surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc...
curvature mean = -0.016, std = 1.234
computing parameterization for surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm...
writing updated template with 1 subjects to my_template0.tif...
2.
%%%
mris_make_template lh sulc 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1)
reading spherical surface
/home/m047599/freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc...
Segmentation fault
3.
%%%
mris_make_template lh curv 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1)
reading spherical surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.curv...
Segmentation fault
4.
%%%
mris_make_template lh sphere 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1)
reading spherical surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sphere...
curvature mean = 0.000, std = 1.000
computing parameterization for surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H...
curvature mean = -0.000, std = 0.602
computing parameterization for surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc...
curvature mean = -0.016, std = 1.234
computing parameterization for surface
../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm...
writing updated template with 1 subjects to my_template0.tif...
To me, Command 1 and 4 are kind of doing the same thing, right?
So I just need to call any one of them, right?
Command 2 and 3 are failed, is it because of my command line?
Actually, the results from command 1 and 4 showed that they have computed sulc,
do I still need run command 2 and command 3 in the "Prep Step"?
Thanks a lot!
Guang
> Date: Fri, 13 Nov 2009 08:15:33 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_make_template question
>
> Hi Guang,
>
> it still needs the ?h.sphere files as those are used to establish the
> spherical coordinate system.
>
> cheers,
> Bruce
> On Thu, 12 Nov 2009, Guang Zeng wrote:
>
> >
> > Hi, there,
> >
> > I am going to make our own template. Based on the introduction in
> > FreeSurfer WIKI "The Surface Registration Process; Template", the first
> > step is "Prep".
> >
> > "The process starts ("Prep") by choosing one reference subject, and
> > producing a template (Here, mytemp0.tif). No ?h.sphere is required --
> > this step uses the subject's own pattern as the reference."
> >
> > Here, I listed my script for this "Prep" step please let me if it is
> > correct:
> >
> > mris_make_template lh smoothwm sample_0 my_template0.tif
> > mris_make_template lh sulc sample_0 my_template0.tif
> > mris_make_template lh curv sample_0 my_template0.tif
> >
> > mris_make_template rh smoothwm sample_0 my_template0.tif
> >
> > mris_make_template rh sulc sample_0 my_template0.tif
> >
> > mris_make_template rh curv sample_0 my_template0.tif
> >
> > Thanks a lot!
> >
> > Guang
> >
> > _
> > Hotmail: Trusted email with powerful SPAM protection.
> > http://clk.atdmt.com/GBL/go/177141665/direct/01/
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] mris_make_template question
Hello, Bruce, Thanks a lot! Now I come to Round. 1, I use command lines below for reference subject # 1 (base_1) %%% mris_register -curv $FREESURFER_HOME/subjects/base_1/surf/lh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_lh.tif $FREESURFER_HOME/subjects/base_1/surf/lh.sphere.myreg0 mris_register -curv $FREESURFER_HOME/subjects/base_1/surf/rh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_rh.tif $FREESURFER_HOME/subjects/base_1/surf/rh.sphere.myreg0 %%% My question is: For reference subject #2 to #N, where should I write output surface file, For example, reference subject #2, base_2 Should my command line be A or B? A. mris_register -curv $FREESURFER_HOME/subjects/base_2/surf/lh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_lh.tif $FREESURFER_HOME/subjects/base_2/surf/lh.sphere.myreg0 B. mris_register -curv $FREESURFER_HOME/subjects/base_2/surf/lh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_lh.tif $FREESURFER_HOME/subjects/base_1/surf/lh.sphere.myreg0 Thanks a lot! Guang > Date: Fri, 13 Nov 2009 13:20:42 -0500 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_make_template question > > no, you shouldn't run 2 and 3. sulc and curv are *not* surface formats, > so the code dies trying to read them as such > On Fri, 13 Nov 2009, Guang Zeng > wrote: > > > > > Hello, Bruce, > > > > Thanks a lot for your help! > > I ran 4 commands, and results are shown below: > > > > 1. > > %%% > > mris_make_template lh smoothwm 018_S_0425_20060419_CN my_template0.tif > > > > creating new parameterization... > > > > processing subject 018_S_0425_20060419_CN (1 of 1) > > reading spherical surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... > > curvature mean = 0.000, std = 1.000 > > computing parameterization for surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... > > curvature mean = -0.000, std = 0.602 > > computing parameterization for surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... > > curvature mean = -0.016, std = 1.234 > > computing parameterization for surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... > > writing updated template with 1 subjects to my_template0.tif... > > > > 2. > > %%% > > mris_make_template lh sulc 018_S_0425_20060419_CN my_template0.tif > > > > creating new parameterization... > > processing subject 018_S_0425_20060419_CN (1 of 1) > > reading spherical surface > > /home/m047599/freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... > > Segmentation fault > > > > 3. > > %%% > > mris_make_template lh curv 018_S_0425_20060419_CN my_template0.tif > > > > creating new parameterization... > > > > processing subject 018_S_0425_20060419_CN (1 of 1) > > reading spherical surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.curv... > > Segmentation fault > > > > 4. > > %%% > > mris_make_template lh sphere 018_S_0425_20060419_CN my_template0.tif > > > > creating new parameterization... > > > > processing subject 018_S_0425_20060419_CN (1 of 1) > > reading spherical surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sphere... > > curvature mean = 0.000, std = 1.000 > > computing parameterization for surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... > > curvature mean = -0.000, std = 0.602 > > computing parameterization for surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... > > curvature mean = -0.016, std = 1.234 > > computing parameterization for surface > > ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... > > writing updated template with 1 subjects to my_template0.tif... > > > > To me, Command 1 and 4 are kind of doing the same thing, right? > > So I just need to call any one of them, right? > > > > Command 2 and 3 are failed, is it because of my command line? > > Actually, the results from co
[Freesurfer] repost a mris_make_template question
Hi, there, I am creating our own template now, and stucked at "Round 1" now (based on FreeSurfer WIKI description http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates). I found a thread posted a year ago and asked the same kind of question, (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08028.html) I read the thread, but still have three questions. I pasted part of the thread here; %% "Hi everyone, We're making a template to register some monkey brain surfaces to. I've written a script based on instructions from the Surface Registration and Templates page ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) on FreeSurfer wiki. I'm stuck at "Round 1" with the "mris_make_template" command. In the first step we used: mris_make_template \ lh sphere \ bu_edited bs_edited vi_edited \ [Command. 1] lh.monk_temp_all.tif As there were no *h.sphere.reg files yes, we used the *h.phere surfaces. My question is, for the next "mris_make_template" should we use the same (*h.sphere) surface or use the newly created *h.sphere.reg surfaces to create the template? mris_make_template \ lh sphere.reg \ bu_edited bs_edited vi_edited \ [Command. 2] lh.monk_temp_all.tif" %% Question. 1, >From my understanding, their template include three subjects "bu_edited", >"bs_edited", "vi_edited", and their command. 1 actually is what FreeSurfer >WIKI called "Prep" step. However, I think in this step, only one subject is needed to create the template "lh.monk_temp_all.tif", am I right ? Actually, Bruce also mentioned that a single subject is used in 1st round, %% Hi Jan, you should use the ?h.sphere.reg on the 2nd round. On our 1st round we use a single subject ?h.sphere to avoid blurring the folding patterns too much, then register all to that one, create the atlas from all the subjects (with the sphere.reg), then recreate all the sphere.reg by reregistering to the 2nd round atlas, then create a 3rd round atlas from the new sphere.reg files. let us know if you need more help. Bruce %% Question. 2, In round. 1, we need call mris_make_template again using all the reference subjects. I think their command. 2 is written for this. However, is this command line correct? I thought it may looks like this: [Command. 3] mris_make_template lh sphere.reg bu_edited lh.monk_temp_all.tif mris_make_template lh sphere.reg bs_edited lh.monk_temp_all.tif mris_make_template lh sphere.reg vi_edited lh.monk_temp_all.tif So which one is correct? Actually, I tried both of them, they all worked. The only difference is the file size of lh.monk_temp_all.tif from Command.2 (1.3 M) is half of the result from Command. 3. (2.7M) Question. 2, If we correctly creat our template, and load it use MATLAB, will the size of the .tif file be 512 x 256 x 9? currently, when I load my .tif files, they are all 512 x 256. Thanks a lot for your help! Guang _ Bing brings you maps, menus, and reviews organized in one place. http://www.bing.com/search?q=restaurants&form=MFESRP&publ=WLHMTAG&crea=TEXT_MFESRP_Local_MapsMenu_Resturants_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to use my own template
Hello, there, I built our own template, and gonna use it to test some subjects. Currently, I have two questions, (1) How can I use my template, In "recon-all.sh", I found that their two places where ?h.average.curvature.filled.buckner40.tif are called, so I just need to change all the "?h.average.curvature.filled.buckner40.tif" in "recon-all.sh" to "?h.average.curvature.filled.owntemplate.tif", is it correct? I think I need not do anything to ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs, right? How about RB_all_withskull_2007-08-08.gca? (2) How can I test if my template is good? I am going to test some subjects using my template and the FS default template, measure the volumes of some ROIS, compare the percentage overlapping ratio and correlation coef, does it sound reasonable? Thanks a lot! Guang _ Windows 7: It works the way you want. Learn more. http://www.microsoft.com/Windows/windows-7/default.aspx?ocid=PID24727::T:WLMTAGL:ON:WL:en-US:WWL_WIN_evergreen:112009v2___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about the output template by make_average_subject
hi, there, I called FS command make_average_subject to create an average subjects using 10 subjects. After the process finished, I found that there are two output template file, "lh.reg.template.tif" and "rh.reg.template.tif". How are these two templates different from the template I built by following the steps described in FS WIKI, The Surface Registration Process; Templates,http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates Thanks a lot! Guang _ Bing brings you maps, menus, and reviews organized in one place. http://www.bing.com/search?q=restaurants&form=MFESRP&publ=WLHMTAG&crea=TEXT_MFESRP_Local_MapsMenu_Resturants_1x1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all -qcache question
Hi, there, I have 60 subjects which have been FS analyzed without the flag -qcache. Now, I wan to do group analysis using QDEC. I need run recon-all -s subjectid -qcache for each of my subjects. Just want to know how it will take to finish the recon-all -s subjectid -qcache command for one subject? Will it go through the whole -autorecon1, 2, 3 process again? Thanks a lot! Guang _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
Hi, there, I have made our own template using 20 subjects follwoing the instruction in FreeSurfer WIKI. (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates). I have a quesition now, Does the quality of the new template depends on the first subject I picked to built the tempalte? Maybe I do not interpret my question clearly, I think I'd like to ask is: If we pick different subject to built a template at the fist step of the all procedure, will the output templates have big difference? If yes, is there a way in FS to pick one subject which is most similar to others, and use it at the first s tep of the build own template procedure? Thanks a lot! Guang _ Chat with Messenger straight from your Hotmail inbox. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_4:092009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to convert our own atlas to freesurfer
Hello, there, We have a manualled labeled atlas, it is saved in a .nii file. We'd liek to use this atlas instead of FS's default atlas. If there are any commands or fucntions in FS can help us to do it. Thanks a lot! Guang _ Windows Live Hotmail gives you a free,exclusive gift. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_7:092009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to convert our own atlas to freesurfer
Hello, Bruce, It is a subcortical structure atlas based on 100 subjects. Thanks a lot! Guang > Date: Wed, 2 Dec 2009 18:32:01 -0500 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to convert our own atlas to freesurfer > > what kind of atlas? > On Wed, 2 Dec 2009, Guang Zeng wrote: > > > > > Hello, there, > > > > We have a manualled labeled atlas, it is saved in a .nii file. > > We'd liek to use this atlas instead of FS's default atlas. If there are > > any commands or fucntions in FS can help us to do it. > > > > Thanks a lot! > > Guang > > > > _ > > Windows Live Hotmail gives you a free,exclusive gift. > > http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_7:092009 _ Windows Live Hotmail is faster and more secure than ever. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_1:092009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to convert our own atlas to freesurfer
Hello, Bruce, Thanks a lot! But which commands I can use to convert our atlas to the .gca format? Guang > Date: Thu, 3 Dec 2009 07:25:29 -0500 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to convert our own atlas to freesurfer > > oh, then you would just replace the .gca file in mri_em_register, > mri_ca_register, mri_ca_label and mri_ca_normalize > > cheers > Bruce > > On Thu, 3 Dec 2009, Guang > Zeng wrote: > > > > > Hello, Bruce, > > > > It is a subcortical structure atlas based on 100 subjects. > > > > > > Thanks a lot! > > Guang > > > >> Date: Wed, 2 Dec 2009 18:32:01 -0500 > >> From: fis...@nmr.mgh.harvard.edu > >> To: freesurfer...@hotmail.com > >> CC: freesurfer@nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] how to convert our own atlas to freesurfer > >> > >> what kind of atlas? > >> On Wed, 2 Dec 2009, Guang Zeng wrote: > >> > >>> > >>> Hello, there, > >>> > >>> We have a manualled labeled atlas, it is saved in a .nii file. > >>> We'd liek to use this atlas instead of FS's default atlas. If there are > >>> any commands or fucntions in FS can help us to do it. > >>> > >>> Thanks a lot! > >>> Guang > >>> > >>> _ > >>> Windows Live Hotmail gives you a free,exclusive gift. > >>> http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_7:092009 > > > > _ > > Windows Live Hotmail is faster and more secure than ever. > > http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_1:092009 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Windows Live Hotmail is faster and more secure than ever. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_1:092009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about the mris_volmask ERROR
Hi, there, I have question about the mris_volmask ERROR. I ran multiple subjects on our SUN Grid Engine system. sometimes some subjects are sent to the same cluster node, and limited memory is assigned to each subject. Because of this, I often met an ERROR at the mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance sub1 step in autorecon3., which gave me an error like: ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x33d05a90): Unable to create a thread. pthread_create() returned 12 I knew this error is caused by some VTK function FS used to allocate memory. What I did is everytime when I met this kind of error, I use recon-all -s subj -autorecon3 -no-isrunning , and the process will finish. However, I found if I did something like this, it will cause problems at the wm parcellation step. For example, I have the same subject which is sent to SGE, fails at mris_volmask, and then I call autorecon3 to finish the process, and I go to wmparc.stats, lotf of rois such as isthumus ctx-cingluate, ctx-posterior singulate are 0. While I ran the same subject at a local machine, and finished without any problems, I looked at isthumus cingluate and posterior singulate, they are not zeros. So, does it mean that I need start from beginning when I met the errors cause by mris_volmask? Thanks a lot! guang _ Chat with Messenger straight from your Hotmail inbox. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_4:092009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_volmask ERROR
Hi, there, I submit several subjects to FS piepline using our Sun Grid Engine System, all of them failed at the same place which is the mris_volmask step in autorecon3. It gave me an error like: ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x33d05a90): Unable to create a thread. pthread_create() returned 12 I knew this error is caused by some VTK function FS used to allocate memory. So what I did is I use recon-all -s subjectid , and the process will finish. What happen is the same subjects have been run on our local machines, and finished without any problems. However, when I looked at the wmparc.stats file of the same subject, the results are quite different. For example, ctx_isthumus cingluate and ctx_posterior singulate value are not zeros for my local machine results, while ctx_isthumus cingluate and ctx_posterior singulate value are zerosfor my SGE machine results. And this problem have to all these subjects. Another funny thing is if I look at the ?h.aparc.stats file, the results from SGE and local machine are the same, while when I load the results to tksurfer, they are quite different. So my question is: Since I need use SGE to run multiple subjects again, next time when I met this mris_volmask ERROR, I need rerun the process from the beginning, not from autorecon3, right? Thank! Guang _ Chat with Messenger straight from your Hotmail inbox. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_4:092009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to load lh.jacobian_white in tkmedit
Hi, there, I'd like to load lh.jacobian_white using tkmedit to check how much the white surface was distorted in order to register to the spherical atlas my command line is tkmedit subj_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.jacobian_white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt But I got an error, === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to analysis-b...@nmr.mgh.harvard.edu : : Now exiting... : Anyone can help? Thanks a lot! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to evaluate our own template without creating our own atlas
Hi, there, We created our own template using 10 subjects, now we'd like to know how good it is compare to FS's default template. We do not create our own atlas yet which need manully label all the regions in the training set. Is there a way to do this kind of comparison? Is it possible to do some kind registration using ?h.white and ?h.sphere. reg, and load the registered ?h.white using tkmedit? Thanks a lot! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qdec output
Hi, there, Does anyone can give me link or paper which explains all the QDEC output file, such as F.mgh, gamma.mgh, beta.mgh ... What are they, how are they related? Thanks a lot! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec output
Hello, Doug, Thanks a lot! I got most of them from the mri_glmfit --help except one, which is maxvox.dat. Is it a way to load this file in tksurfer? Thanks a lot! Guang > Date: Mon, 14 Dec 2009 18:35:39 -0500 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qdec output > > Try running mri_glmfit with the --help option. QDEC runs mri_glmfit. > > doug > > Guang Zeng wrote: > > Hi, there, > > > > Does anyone can give me link or paper which explains all the QDEC > > output file, such as F.mgh, gamma.mgh, beta.mgh ... > > What are they, how are they related? > > > > Thanks a lot! > > Guang > > > > > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > > now. <http://clk.atdmt.com/GBL/go/171222985/direct/01/> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about mris_ca_train
Hi, there, Recently, I sent sseveral emails to you to ask same kind of question about building our own template and atlas. Thanks a lot for your quick reply, they helps me a lot. Currently, I still have a question about building our own atlas using mris_ca_train, sorry to bother you again. We have a surface labeling atlas in our lab, we'd like to use this atlas instead of using FS's desikan_killiany.2007-06-20gcs. It is kind of difficult for us to load every subject in our training set to tksurfer, and manually label each ROI based on our ATLAS. What we try to do is: 1. Send each subject in the training set to our toolbox which will use our atlas to do surface labeling. For each subject it will output a file just like wmparc.mgz in FS, but it is NIfTI file. 2. Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc files. 3. Find a method to get my ?h. mylabels. annot files, and use mris_ca_train to build a new atlas. First of all, do you think what I try to do is reasonable? If yes, I know I need to get the FS .label files for each ROI, then I can call mris_label2annot to get ?h. mylabels. annot files. But how can I get the FS .label files for each ROI from our toolbox output ROI labeled NIfTI file? These qurstions trouble me for a long time, your help are really appreciate. Thanks a lot! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] a question about mris_ca_train
Hello, there, If I have the label file of a ROI, and I want to convert the RAS coordinate of each vertex to volume index, which command I can use? Thanks! Guang > Date: Fri, 18 Dec 2009 14:18:44 -0500 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Subject: Re: [Freesurfer] a question about mris_ca_train > > I don't have any more suggestions except to play with the projection > fraction. You can load the data simultaneously in tkmedit and tksurfer, > click on a hole in tksurfer, then use the "Save/Go To Point" feature to > see in tkmedit why the surface does not pass through your label. > > doug > > Guang Zeng wrote: > > Hello, Doug, > > > > Thanks a lot for your suggestion, I added --projfrac 0.5 to my > > vol2surf command, > > the result looks much better now, but there are still some regions > > among ROIs have no label, > > please see the attached figure. > > > > Could you give some suggestions to fix this problem. > > Thanks a lot! > > Guang > > > > > Date: Thu, 17 Dec 2009 12:22:28 -0500 > > > From: gr...@nmr.mgh.harvard.edu > > > To: freesurfer...@hotmail.com > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > When you run vol2surf, try specifying --projfrac 0.5 to sample in the > > > middle of the ribbon. > > > > > > doug > > > > > > Guang Zeng wrote: > > > > Hello, Doug, > > > > > > > > Fix that dimension dismtach problem now, and got my annot.file, but I > > > > still have problems, > > > > I attached the images which show my atals and annotation file loaded > > > > into tkmedit and tksurfer, the surface is > > > > broken. > > > > > > > > Could you tell me what I need to do? > > > > > > > > Thanks a lot! > > > > Guang > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 18:05:03 -0500 > > > > > From: gr...@nmr.mgh.harvard.edu > > > > > To: freesurfer...@hotmail.com > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > Load it again in tkmedit to make sure you have the color table > > right, > > > > > then re-run you mris_seg2annot command with your color table. > > > > > > > > > > doug > > > > > > > > > > Guang Zeng wrote: > > > > > > Hello, Doug, > > > > > > > > > > > > I am transfering my color lookup table to FreeSurfer ColorLUT > > now. It > > > > > > may need a little while. > > > > > > I load the a.anat.mgz using tkmedit and FreeSurfer lookup table, > > > > > > although the label and the colors looks a little bit > > > > > > strange, but all the other things look fine to me such as the > > > > > > segmentation results are registered pretty well. > > > > > > > > > > > > Could you tell me what I need to do next, once my color lookup > > table > > > > > > is ready, > > > > > > > > > > > > Thanks! > > > > > > Guang > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 17:39:07 -0500 > > > > > > > From: gr...@nmr.mgh.harvard.edu > > > > > > > To: freesurfer...@hotmail.com > > > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > > > > > First, work in the volume instead of the surface because the > > > > surface is > > > > > > > too hard to determine what is going on. Convert a.nii to the > > > > anatomical > > > > > > > space with > > > > > > > > > > > > > > mri_vol2vol --mov a.nii --reg > > > > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat --interp > > > > > > > nearest --fstarg \ > > > > > > > --o $FREESURFER_HOME/subjects/sub1/mri/a.anat.mgz > > > > > > > > > > > > > > Then look at the output in tkmedit: > > > > > > > > > > > > > > tkmedit sub1 orig.mgz -surfs -seg a.anat.mgz YOURLUT > > > > > > > > > > > > > > where YOURLUT is a color lookup table for your segmentation > > > > (model it > > >
[Freesurfer] question about mris_ca_train
Hi, there, I have created our own template and am creating our own atlas now. I have annotation files for each subject in my training set, and my mris_ca_train command line is: mris_ca_train -n 2 -t /home/freesurfer-install/freesurfer/ATLASColorLUT.txt lh sphere.reg myatalas.annot custom_1 custom_2 custom_3 custom_4 lh_myatlas.gcs my question is here, I should use the lh.sphere.reg file which register the sphere to the FS default template or the registration file which register the sphere to my own template? Thanks! Guang _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390707/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] manually labeled subjects used for building the desikan_killiany gcs file
Hello, there, If it possible that I can view or download the manually labeled subjects you used for building the desikan_killiany gcs file from somewhere in the wiki? Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/196390710/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about rebuild_gca_atlas.csh
Hi, there, In rebuild_gca_atlas.csh, I read something like: # A talairach registration should be generated for this first subject as well, # in order to align the final atlas to the Talairach space. Is this talairach registration file the same as the talairach.xfm under each subject's /mri/transforms/ direcotry? Thanks! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurfer two atalses
Hi, there, Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer need to atlases; Subcortical and Surface? Thanks! Guang _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] license problem
Hi, there, I installed FreeSurfer under my local directory few months ago. Last week, I copied all the FreeSurfer folder under my local directory (include .license file) to the /home directory of our group, so everyone can use it. However, it turns out that they can not use it even they can see the .license in the /home directory through their machine. So do I need reinstall Freesurfer under our /home directory, instead of just copy? Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/196390708/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] images with poor resolution
Hello, Nick, I read your answer to this thread posted few months ago. Currently, I met the same kind of problem, and I used the method you recommended below, it works pretty well on my cases. My question is: The results of my data have been improved in FS cross-sectional stream, if I want to send them to the FS longitudinal stream, Could I just need follow the general FS longitudinal stream or I still need the -expert /xopts.txt and -seg-wlo wlo -seg-ghi ghi options somewhere in the longitudinal stream? Thanks! Guang > From: ni...@nmr.mgh.harvard.edu > To: dwm2...@med.cornell.edu; freesurfer@nmr.mgh.harvard.edu > Date: Mon, 5 Oct 2009 19:11:15 -0400 > Subject: Re: [Freesurfer] images with poor resolution > > Dana, > > First I would run: > > recon-all -s subid -clean > > to remove any prior control points and edits. > > Then I would open nu.mgz: > > tkmedit subjid nu.mgz > > and *sparingly* put control points well into white matter areas on a few > different slices. you only need a half dozen or so. to add control > points, see: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints > > except you will add them to nu.mgz, to make sure that T1.mgz gets > created properly. > > Then create a file name xopts.txt containing these lines: > > mri_normalize -gentle > > Then run: > > recon-all -s subjid -autorecon1 -expert /xopts.txt > > and when done, open brainmask.mgz > > tkmedit subjid brainmask.mgz > > and check again to get a sense of the low value for white matter and > high value for gray matter, then run: > > recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi > > replacing wlo and ghi with those values. > > if the surfaces still look bad, you can add a line to the xopts.txt > file : > > mris_make_surfaces -max_gray val -min_gray_at_white_border val > > replacing the two 'val's with something you find appropriate, then run: > > recon-all -s subjid -autorecon2-pial -autorecon3 \ > -expert /xopts.txt > > good luck! > > Nick > > > On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > > Hi Nick, > > > > Below is Bruce's response to a problem I'm having with the gray/white > > segmentation. (Pasted below, you can see the brainmask.mgz volume and > > surfaces--the entire brain is labeled as white matter). I could use > > some guidance in carrying out his advice. He says to adjust the > > intensity normalization using control points and then use expert opts > > for mri_segment and mris_make_surfaces. > > > > When I look at the brain.mgz volume, the white matter tends to have an > > intensity of 110, as it should, but the gray matter at times goes as > > high as 115. I was thinking, I could set ghi to 115 and wlo to 110. > > Then, I am not sure how to actually run the corrections and what > > language to use to implement the control points and mri_segment > > adjustments. I will save control points and then run: recon-all > > -autorecon2-cp -autorecon3 -subjed . Can I somehow include > > the mri_segment adjustments into this command, or do I have to run > > that separately? > > > > I am also not sure how options for mris_make_surfaces might help. > > > > I appreciate your help with this! > > > > Thanks, > > dana > > > > > > > > > > [] > > > > At 04:40 PM 10/2/2009, Bruce Fischl wrote: > > > Hi Dana, > > > > > > it looks like the gray/white density estimation failed. Try setting > > > them with the expert opts for mri_segment and mris_make_surfaces > > > (Nick can point you in the right direction if you can't figure it > > > out). Things like max gm at white border and such. > > > > > > cheers, > > > Bruce > > > > > > p.s. it also looks like the intensity normalization went too far due > > to the low contrast. You'll probably need to add some control points > > and run it with the -gentle option > > > > > > > > > On Fri, 2 Oct 2009, Dana W. Moore wrote: > > > > > > > Hi everyone, > > > > > > > > I am trying to salvage some images that were done with poor > > > > gray/white boundary contrasts. First, FreeSurfer includes an area > > > > of dura in the skull strip. I tried adjusting the watershed but > > > > it made no differences. FreeSurfer is subsequently unable to > > > > detect the gray/white boundary and labels the dura as cortex: > > > > > > > > [] > > > > > > > > > > > > > > > > Looking at the raw images, the gray/white boundaries are faint but > > > > visible. Is there anything I can adjust to try to make this work > > > > with FreeSurfer? > > > > > > > > Thanks, > > > > Dana > > > > > > > > > > > > Dana W. Moore, Ph.D. > > > > Neuropsychology Fellow > > > > Cornell Neuropsychology Service > > > > Weill Medical College of Cornell University > > > > New York Presbyterian Hospital > > > > Department of Neurology & Neuroscience > > > > 428 East 72nd Street, Suite 500 > > > > New York, NY 10021 > > > > Phone: 212-746-2823 > > > > Fax: 212-746-5584 > > > > Email: dwm2...@med.cornell.edu > > > > Dana W. Moore, Ph.D
[Freesurfer] a question about control points
Hi, there, I have some scans which have poor white matter and gray matter contrast, and the results of the intensity normalization step are pretty bad. So I add some controls, the results looks much better now. But I met a question now, I sent these results-improved subjects to FS longitudinal stream without those controls points, the longitudinal results are as bad as before. My command line is: recon-all -base subj_based_id -tp subj1 -tp subj2 -all recon-all -long subj1 subj_base -all recon-all -long subj2 subj_base -all I think the problem is the FS surfer longitudinal stream will copy the orig.mgz of each time point, map them to the base template, and then go through FS stream again. How can I map my added control points to the base template, and use them in the longitudinal stream, or I should map it to somewhere at the recon-all -base subj_based_id -tp subj1 -tp subj2 -all step. Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/196390708/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] images with poor resolution
Hello, Nick, I am using the latest 4.5.0. So I only need add those -seg-wlo -segwhi flags at the "-long" step, not the "-base" step, right? Thank! Guang > Subject: RE: [Freesurfer] images with poor resolution > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Date: Mon, 25 Jan 2010 11:18:07 -0500 > > the longitudinal stream will take any controls points added to the > cross-sectional stream, but will not take any expert options or special > -seg-wlo -segwhi flags, so you would have to add those yourself to the > longitudinal stream. > > On Sat, 2010-01-23 at 22:02 -0600, Guang Zeng wrote: > > Hello, Nick, > > > > I read your answer to this thread posted few months ago. > > Currently, I met the same kind of problem, and I used the method you > > recommended below, it works pretty well on my cases. > > My question is: > > > > The results of my data have been improved in FS cross-sectional > > stream, if I want to send them to the FS longitudinal stream, > > Could I just need follow the general FS longitudinal stream or I still > > need the -expert /xopts.txt and -seg-wlo wlo -seg-ghi ghi > > options > > somewhere in the longitudinal stream? > > > > Thanks! > > Guang > > > > > > > > > From: ni...@nmr.mgh.harvard.edu > > > To: dwm2...@med.cornell.edu; freesurfer@nmr.mgh.harvard.edu > > > Date: Mon, 5 Oct 2009 19:11:15 -0400 > > > Subject: Re: [Freesurfer] images with poor resolution > > > > > > Dana, > > > > > > First I would run: > > > > > > recon-all -s subid -clean > > > > > > to remove any prior control points and edits. > > > > > > Then I would open nu.mgz: > > > > > > tkmedit subjid nu.mgz > > > > > > and *sparingly* put control points well into white matter areas on a > > few > > > different slices. you only need a half dozen or so. to add control > > > points, see: > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints > > > > > > except you will add them to nu.mgz, to make sure that T1.mgz gets > > > created properly. > > > > > > Then create a file name xopts.txt containing these lines: > > > > > > mri_normalize -gentle > > > > > > Then run: > > > > > > recon-all -s subjid -autorecon1 -expert /xopts.txt > > > > > > and when done, open brainmask.mgz > > > > > > tkmedit subjid brainmask.mgz > > > > > > and check again to get a sense of the low value for white matter and > > > high value for gray matter, then run: > > > > > > recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi > > > > > > replacing wlo and ghi with those values. > > > > > > if the surfaces still look bad, you can add a line to the xopts.txt > > > file : > > > > > > mris_make_surfaces -max_gray val -min_gray_at_white_border val > > > > > > replacing the two 'val's with something you find appropriate, then > > run: > > > > > > recon-all -s subjid -autorecon2-pial -autorecon3 \ > > > -expert /xopts.txt > > > > > > good luck! > > > > > > Nick > > > > > > > > > On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > > > > Hi Nick, > > > > > > > > Below is Bruce's response to a problem I'm having with the > > gray/white > > > > segmentation. (Pasted below, you can see the brainmask.mgz volume > > and > > > > surfaces--the entire brain is labeled as white matter). I could > > use > > > > some guidance in carrying out his advice. He says to adjust the > > > > intensity normalization using control points and then use expert > > opts > > > > for mri_segment and mris_make_surfaces. > > > > > > > > When I look at the brain.mgz volume, the white matter tends to > > have an > > > > intensity of 110, as it should, but the gray matter at times goes > > as > > > > high as 115. I was thinking, I could set ghi to 115 and wlo to > > 110. > > > > Then, I am not sure how to actually run the corrections and what > > > > language to use to implement the control points and mri_segment > > > > adjustments. I will save control points and then run: recon-all > > > >
Re: [Freesurfer] images with poor resolution
Hi, there, Does the -base step of FreeSurfer also contains three step, and can be called through recon-all as recon-all.. -autorecon1, recon-all .. -autorecon2, recon-all .. -autorecon3 Thanks! > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Date: Mon, 25 Jan 2010 12:34:47 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] images with poor resolution > > also the base step > > On Mon, 2010-01-25 at 10:41 -0600, Guang Zeng wrote: > > Hello, Nick, > > > > I am using the latest 4.5.0. > > So I only need add those -seg-wlo -segwhi flags at the "-long" step, > > not the "-base" step, right? > > > > Thank! > > Guang > > > > > Subject: RE: [Freesurfer] images with poor resolution > > > From: ni...@nmr.mgh.harvard.edu > > > To: freesurfer...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Date: Mon, 25 Jan 2010 11:18:07 -0500 > > > > > > the longitudinal stream will take any controls points added to the > > > cross-sectional stream, but will not take any expert options or > > special > > > -seg-wlo -segwhi flags, so you would have to add those yourself to > > the > > > longitudinal stream. > > > > > > On Sat, 2010-01-23 at 22:02 -0600, Guang Zeng wrote: > > > > Hello, Nick, > > > > > > > > I read your answer to this thread posted few months ago. > > > > Currently, I met the same kind of problem, and I used the method > > you > > > > recommended below, it works pretty well on my cases. > > > > My question is: > > > > > > > > The results of my data have been improved in FS cross-sectional > > > > stream, if I want to send them to the FS longitudinal stream, > > > > Could I just need follow the general FS longitudinal stream or I > > still > > > > need the -expert /xopts.txt and -seg-wlo wlo -seg-ghi ghi > > > > options > > > > somewhere in the longitudinal stream? > > > > > > > > Thanks! > > > > Guang > > > > > > > > > > > > > > > > > From: ni...@nmr.mgh.harvard.edu > > > > > To: dwm2...@med.cornell.edu; freesurfer@nmr.mgh.harvard.edu > > > > > Date: Mon, 5 Oct 2009 19:11:15 -0400 > > > > > Subject: Re: [Freesurfer] images with poor resolution > > > > > > > > > > Dana, > > > > > > > > > > First I would run: > > > > > > > > > > recon-all -s subid -clean > > > > > > > > > > to remove any prior control points and edits. > > > > > > > > > > Then I would open nu.mgz: > > > > > > > > > > tkmedit subjid nu.mgz > > > > > > > > > > and *sparingly* put control points well into white matter areas > > on a > > > > few > > > > > different slices. you only need a half dozen or so. to add > > control > > > > > points, see: > > > > > > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints > > > > > > > > > > except you will add them to nu.mgz, to make sure that T1.mgz > > gets > > > > > created properly. > > > > > > > > > > Then create a file name xopts.txt containing these lines: > > > > > > > > > > mri_normalize -gentle > > > > > > > > > > Then run: > > > > > > > > > > recon-all -s subjid -autorecon1 -expert /xopts.txt > > > > > > > > > > and when done, open brainmask.mgz > > > > > > > > > > tkmedit subjid brainmask.mgz > > > > > > > > > > and check again to get a sense of the low value for white matter > > and > > > > > high value for gray matter, then run: > > > > > > > > > > recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi > > > > > > > > > > replacing wlo and ghi with those values. > > > > > > > > > > if the surfaces still look bad, you can add a line to the > > xopts.txt > > > > > file : > > > > > > > > > > mris_make_surfaces -max_gray val -min_gray_at_white_border val > > > > > > > > > > replacing the two 'val's wit
Re: [Freesurfer] images with poor resolution
Hi, there, Does the -base step of the FreeSurfer longitudinal stream also contains three step, and can be called through recon-all as recon-all -base .. -autorecon1, recon-all -base .. -autorecon2, recon-all -base.. -autorecon3 Thanks! From: freesurfer...@hotmail.com To: ni...@nmr.mgh.harvard.edu Date: Mon, 25 Jan 2010 13:57:58 -0600 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] images with poor resolution Hi, there, Does the -base step of FreeSurfer also contains three step, and can be called through recon-all as recon-all.. -autorecon1, recon-all .. -autorecon2, recon-all .. -autorecon3 Thanks! > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Date: Mon, 25 Jan 2010 12:34:47 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] images with poor resolution > > also the base step > > On Mon, 2010-01-25 at 10:41 -0600, Guang Zeng wrote: > > Hello, Nick, > > > > I am using the latest 4.5.0. > > So I only need add those -seg-wlo -segwhi flags at the "-long" step, > > not the "-base" step, right? > > > > Thank! > > Guang > > > > > Subject: RE: [Freesurfer] images with poor resolution > > > From: ni...@nmr.mgh.harvard.edu > > > To: freesurfer...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Date: Mon, 25 Jan 2010 11:18:07 -0500 > > > > > > the longitudinal stream will take any controls points added to the > > > cross-sectional stream, but will not take any expert options or > > special > > > -seg-wlo -segwhi flags, so you would have to add those yourself to > > the > > > longitudinal stream. > > > > > > On Sat, 2010-01-23 at 22:02 -0600, Guang Zeng wrote: > > > > Hello, Nick, > > > > > > > > I read your answer to this thread posted few months ago. > > > > Currently, I met the same kind of problem, and I used the method > > you > > > > recommended below, it works pretty well on my cases. > > > > My question is: > > > > > > > > The results of my data have been improved in FS cross-sectional > > > > stream, if I want to send them to the FS longitudinal stream, > > > > Could I just need follow the general FS longitudinal stream or I > > still > > > > need the -expert /xopts.txt and -seg-wlo wlo -seg-ghi ghi > > > > options > > > > somewhere in the longitudinal stream? > > > > > > > > Thanks! > > > > Guang > > > > > > > > > > > > > > > > > From: ni...@nmr.mgh.harvard.edu > > > > > To: dwm2...@med.cornell.edu; freesurfer@nmr.mgh.harvard.edu > > > > > Date: Mon, 5 Oct 2009 19:11:15 -0400 > > > > > Subject: Re: [Freesurfer] images with poor resolution > > > > > > > > > > Dana, > > > > > > > > > > First I would run: > > > > > > > > > > recon-all -s subid -clean > > > > > > > > > > to remove any prior control points and edits. > > > > > > > > > > Then I would open nu.mgz: > > > > > > > > > > tkmedit subjid nu.mgz > > > > > > > > > > and *sparingly* put control points well into white matter areas > > on a > > > > few > > > > > different slices. you only need a half dozen or so. to add > > control > > > > > points, see: > > > > > > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints > > > > > > > > > > except you will add them to nu.mgz, to make sure that T1.mgz > > gets > > > > > created properly. > > > > > > > > > > Then create a file name xopts.txt containing these lines: > > > > > > > > > > mri_normalize -gentle > > > > > > > > > > Then run: > > > > > > > > > > recon-all -s subjid -autorecon1 -expert /xopts.txt > > > > > > > > > > and when done, open brainmask.mgz > > > > > > > > > > tkmedit subjid brainmask.mgz > > > > > > > > > > and check again to get a sense of the low value for white matter > > and > > > > > high value for gray matter, then
[Freesurfer] FW: images with poor resolution
Hello, Nick, Thanks a lot. The reason I ask is because in your previous reply to the "images with poor resolution" thread, you explained that in order to fix the problem, we need first (1) add ctr points, then run recon-all -s subjid -autorecon1 -expert /xopts.txt (2) check again to get a sense of the low value for white matter and high value for gray matter, then run: recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi It looks to me that I can not use -all directly here at the -base step, I had to do it step by step. That's why I need to know if the -base step is divided to three steps and three steps only. Thanks! Guang > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > Date: Mon, 25 Jan 2010 16:17:43 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] images with poor resolution > > -base triggers creation of the base subject, and requires the usual > additional flags to run the entire stream. -all is the what is > recommended here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing > > but you could also run the stages separately. > > > On Mon, 2010-01-25 at 15:05 -0600, Guang Zeng wrote: > > Hi, there, > > > > Does the -base step of the FreeSurfer longitudinal stream also > > contains three step, > > and can be called through recon-all as recon-all -base .. > > -autorecon1, > > > > recon-all -base .. -autorecon2, > > recon-all > > -base.. -autorecon3 > > > > Thanks! > > > > > > > > __ > > From: freesurfer...@hotmail.com > > To: ni...@nmr.mgh.harvard.edu > > Date: Mon, 25 Jan 2010 13:57:58 -0600 > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] images with poor resolution > > > > Hi, there, > > > > Does the -base step of FreeSurfer also contains three step, and can be > > called through recon-all as recon-all.. -autorecon1, > > recon-all .. -autorecon2, recon-all .. -autorecon3 > > > > Thanks! > > > > > From: ni...@nmr.mgh.harvard.edu > > > To: freesurfer...@hotmail.com > > > Date: Mon, 25 Jan 2010 12:34:47 -0500 > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] images with poor resolution > > > > > > also the base step > > > > > > On Mon, 2010-01-25 at 10:41 -0600, Guang Zeng wrote: > > > > Hello, Nick, > > > > > > > > I am using the latest 4.5.0. > > > > So I only need add those -seg-wlo -segwhi flags at the "-long" > > step, > > > > not the "-base" step, right? > > > > > > > > Thank! > > > > Guang > > > > > > > > > Subject: RE: [Freesurfer] images with poor resolution > > > > > From: ni...@nmr.mgh.harvard.edu > > > > > To: freesurfer...@hotmail.com > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > Date: Mon, 25 Jan 2010 11:18:07 -0500 > > > > > > > > > > the longitudinal stream will take any controls points added to > > the > > > > > cross-sectional stream, but will not take any expert options or > > > > special > > > > > -seg-wlo -segwhi flags, so you would have to add those yourself > > to > > > > the > > > > > longitudinal stream. > > > > > > > > > > On Sat, 2010-01-23 at 22:02 -0600, Guang Zeng wrote: > > > > > > Hello, Nick, > > > > > > > > > > > > I read your answer to this thread posted few months ago. > > > > > > Currently, I met the same kind of problem, and I used the > > method > > > > you > > > > > > recommended below, it works pretty well on my cases. > > > > > > My question is: > > > > > > > > > > > > The results of my data have been improved in FS > > cross-sectional > > > > > > stream, if I want to send them to the FS longitudinal stream, > > > > > > Could I just need follow the general FS longitudinal stream or > > I > > > > still > > > > > > need the -expert /xopts.txt and -seg-wlo wlo -seg-ghi > > ghi > > > > > > options > > > > > > somewhere in the longitudinal stream? > > > > > > >
[Freesurfer] a question abourt FS longitudinal stream
Hi, there, I have a question about FS longitudinal stream, Suppose I have two volumes A and B, B is the copy of A, but has been scaled (say, 1%) at each direction. Both of them have been cross-sectionally processed. If we send them to the FS longitudinal stream, what will happen? For example, if we look at the hippocampal volume of A and B (longitudinal result), Should their percentage difference be around 0% or 3%? Thanks! Guang _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390707/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to view .gca file
Hello, Bruce,
Thanks for your reply. I still have two questions,
1. Does these gca files also include 9 arrays such as those template files
saved into .tiff file.
Is there any place in the WIKI explain the format of the gca files?
What is the difference between gca#0 and gca#1?
2. I tried the command line you suggested,
mri_convert atlas.gca#1 priors.mgz labels.mgz
It gave me an error message:
mri_convert: extra argument ("labels.mgz")
type mri_convert -u for usage
Thanks a lot!
Guang
> Date: Thu, 29 Oct 2009 07:21:42 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] (no subject)
>
> you can load it in tkmedit from the file menu and probe it one voxel at a
> time, or you can use
>
> mri_convert atlas.gca#0 means.mgz
>
> and
>
> mri_convert atlas.gca#1 priors.mgz labels.mgz
>
> to look at the most likely label and it's mean
>
> cheers,
> Bruce
>
> On Thu, 29 Oct 2009, Guang Zeng
> wrote:
>
> >
> > Hi, there,
> >
> > I want to know how the FS GCA atlas looks like, is there a way to load the
> > FS GCA Atlas and view it using tkmedit or matlab?
> >
> > Is it possible to replace FS Atlas with our own Atlas and use it for
> > analysis?
> >
> > Thanks a lot!
> > Guang
> >
> > _
> > New Windows 7: Find the right PC for you. Learn more.
> > http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID24727::T:WLMTAGL:ON:WL:en-US:WWL_WIN_pcscout:102009
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Re: [Freesurfer] how to view .gca file
Hello, Bruce,
Thanks a lot for your quick reply?
Could I ask what is the difference between labels.mgz and priors.mgz (or
atlas.gca#1 and atlas.gca#2).
I load both of them in tkmedit, move the mouse in the image, they all gave me
the same value.
Thanks!
Guang
> Date: Thu, 28 Jan 2010 16:51:56 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] how to view .gca file
>
> Hi Guang,
>
> it should be:
>
> mri_convert atlas.gca#0 means.mgz
> mri_convert atlas.gca#1 labels.mgz
> mri_convert atlas.gca#2 priors.mgz
>
> cheers,
> Bruce
>
> p.s. sorry, I don't think the gca format is documented anywhere, but you
> are welcome to the code if you want
>
> On Thu, 28 Jan 2010, Guang Zeng wrote:
>
> >
> > Hello, Bruce,
> >
> > Thanks for your reply. I still have two questions,
> >
> > 1. Does these gca files also include 9 arrays such as those template files
> > saved into .tiff file.
> > Is there any place in the WIKI explain the format of the gca files?
> >
> > What is the difference between gca#0 and gca#1?
> >
> > 2. I tried the command line you suggested,
> >
> > mri_convert atlas.gca#1 priors.mgz labels.mgz
> >
> > It gave me an error message:
> >
> > mri_convert: extra argument ("labels.mgz")
> >
> > type mri_convert -u for usage
> >
> > Thanks a lot!
> > Guang
> >
> >> Date: Thu, 29 Oct 2009 07:21:42 -0400
> >> From: fis...@nmr.mgh.harvard.edu
> >> To: freesurfer...@hotmail.com
> >> CC: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] (no subject)
> >>
> >> you can load it in tkmedit from the file menu and probe it one voxel at a
> >> time, or you can use
> >>
> >> mri_convert atlas.gca#0 means.mgz
> >>
> >> and
> >>
> >> mri_convert atlas.gca#1 priors.mgz labels.mgz
> >>
> >> to look at the most likely label and it's mean
> >>
> >> cheers,
> >> Bruce
> >>
> >> On Thu, 29 Oct 2009, Guang Zeng
> >> wrote:
> >>
> >>>
> >>> Hi, there,
> >>>
> >>> I want to know how the FS GCA atlas looks like, is there a way to load
> >>> the FS GCA Atlas and view it using tkmedit or matlab?
> >>>
> >>> Is it possible to replace FS Atlas with our own Atlas and use it for
> >>> analysis?
> >>>
> >>> Thanks a lot!
> >>> Guang
> >>>
> >>> _
> >>> New Windows 7: Find the right PC for you. Learn more.
> >>> http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID24727::T:WLMTAGL:ON:WL:en-US:WWL_WIN_pcscout:102009
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > _
> > Hotmail: Trusted email with Microsoft?s powerful SPAM protection.
> > http://clk.atdmt.com/GBL/go/196390706/direct/01/
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[Freesurfer] Is there a bash version of rebuild_gca_atlas.csh
Hello, there, Is there a bash version of rebuild_gca_atlas.csh? Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/196390710/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] rebuild_gca_atlas.csh question
Hi, there, I am running rebuild_gca_atlas.csh now, and met a problem at the first mri_ca_normalize step, my rebuild_gca_atlas.log file looks like below, \n\n mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/norm.mgz mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/norm.mgz mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/norm.mgz mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/norm.mgz \n\n .. Is this noatlas noxform valid here, should it be -noatlas -noxform? Actually, what I got from my terminal is; Log file is /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/rebuild_gca_atlas_2010-02-01.log mri_ca_normalize each subject using its seg_edited.mgz, producing norm.mgz... mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/bra: No such file or directory mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0413_20060502: No such file or directory mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_0559_20060523: No such file or directory mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/brain.mgz -seg /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/seg_edited.mgz /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/nu.mgz noatlas noxform /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129/mri/norm.mgz Unable to read script file because of error: error opening mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/002_S_1018_20061129: No such file or directory But all the files and directories are there? any suggestions? Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/
[Freesurfer] why FreeSurfer Surface Atlas does not contain subcortical region
Hi, there, Kind of wondering, why FreeSurfer Surface Atlas does not contain subcortical region? Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurferColorLUT label Unkown in annotation file
Hi, there, I have question about FreeSurferColorLUT label Unkown in annotation file. In FreeSurferColorLUT, I read that #No. Label Name:R G B A 0 Unknown 0 00 0 I load the inflated surface of a subject, import lh.aparc.annot file. All the subcortical region are labelled as "Unknown" Then I load the lh.aparc.annot file using read_annotation.m to MATLAB as [vertices, label_val, colortable] = read_annotation(annotation_filename); Since the RGB of label Unknown is zero, then its label value in read_annotation.m should also be zero, since annotation value = (R) + (G * 256) + (B * 256^2) However, there are no vertices with label_val = 0 when I use unknown = find(label_val == 0). I also check the label_val of several randomly picked verteices in unkown (subcortical) region, they gave me different values. I thought I should find the same values, although they may not equal to zero. So, my question is how to find the vertices which are labelled as unknown in annotation file? Thanks! Guang _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469226/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] where can I find write_annotation.m
Hello, there, Where can I download write_annotation.m, I can not find it in my /matlab folder. Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] a question about mris_ca_train
Hello, Doug, Thanks a lot for your reply. What you said is correct. I saw those non-connected or non-contiguous labels which show as 'No label' when I import the annotation file. Two questions: 1. If I want to use my own annotation files to create own surface atlas, all the vertices stored in my annotation files should have a label? 2. What is the label for those vertices shown as 'No label'? Or they will not be written in the annotation file? Thanks! Guang > Date: Wed, 16 Dec 2009 13:12:59 -0500 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] a question about mris_ca_train > > You can use mri_vol2surf with the --interp nearest option to sample your > volume segmentations onto the surface. You can then use mris_seg2annot > to convert this segmentation directly to an annotation, then use > mri_annotation2label to convert the annotation into a set of labels. > Nothing here guarantees that labels will be connected or contiguous nor > is it sure that all vertices on the surface will be labeled. > > doug > > Guang Zeng wrote: > > Hi, there, > > > > Recently, I sent sseveral emails to you to ask same kind of question > > about building our own template and atlas. > > Thanks a lot for your quick reply, they helps me a lot. > > > > Currently, I still have a question about building our own atlas using > > mris_ca_train, sorry to bother you again. > > > > We have a surface labeling atlas in our lab, we'd like to use this > > atlas instead of using FS's desikan_killiany.2007-06-20gcs. > > It is kind of difficult for us to load every subject in our training > > set to tksurfer, and manually label each ROI based on our ATLAS. > > > > What we try to do is: > > 1. Send each subject in the training set to our toolbox which will use > > our atlas to do surface labeling. For each subject it will output a > > file just like > > wmparc.mgz in FS, but it is NIfTI file. > > > > 2. Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc > > files. > > > > 3. Find a method to get my ?h. mylabels. annot files, and use > > mris_ca_train to build a new atlas. > > > > First of all, do you think what I try to do is reasonable? > > > > If yes, I know I need to get the FS .label files for each ROI, then I > > can call mris_label2annot to get ?h. mylabels. annot files. > > > > But how can I get the FS .label files for each ROI from our toolbox > > output ROI labeled NIfTI file? > > > > These qurstions trouble me for a long time, your help are really > > appreciate. > > > > Thanks a lot! > > Guang > > > > > > > > > > > > > > > > > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > > now. <http://clk.atdmt.com/GBL/go/171222985/direct/01/> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to QC hippocampal measurement
Hi, there, I have used FreeSurfer to measure the hippocampal size of 200 ADNI subjects, and now I'd like to QC the hippocampal measurement. Anyone can give me some suggestion to do this, instead of loading they one-by-one ? Thanks! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] diagnostic level
Hi, there, Both mris_ca_label and mris_ca_train have a -v option which is called: diagnostic level. What is the meaning of this diagnostic level? Thanks! Guang _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469227/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer fill holes
Hi, there, Is there are a command-line version of that 'Fill holes", "Dilate" and "Erode" options in tksurfer. Could I select the size of the kernel for dilation and erosion? Thanks! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about rebuild_gca_atlas.csh
Hi, there, I am using the rebuild_gca_atlas.csh to build our own subcortical atals now, and met a problem at the second step which is # Train using ONE_SUBJECT, the command line is: mri_ca_train -prior_spacing 2 -node_spacing 8 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_man.xfm -T1 norm.mgz -check $OneID /data1/radiology/m047599/temp_fs_2/freesurfer-v4.5.0/subjects/average/RB_12-Feb-2010.gca and it gave me errors such as; ERROR: Left_Caudate: 104 167 182, tal *** x=22.896236 > 5 ***, y=33.105412, z=-16.869007 ERROR: Left_Caudate: 104 167 183, tal *** x=22.900818 > 5 ***, y=34.053909, z=-16.893997 ERROR: Left_Caudate: 104 167 184, tal *** x=22.905401 > 5 ***, y=35.002407, z=-16.918985 ERROR: Left_Caudate: 104 167 185, tal *** x=22.909985 > 5 ***, y=35.950901, z=-16.943975 ERROR: Left_Caudate: 104 167 186, tal *** x=22.914564 > 5 ***, y=36.899403, z=-16.968966 ERROR: Left_Caudate: 104 167 187, tal *** x=22.919147 > 5 ***, y=37.847897, z=-16.993954 ERROR: Left_Caudate: 104 167 188, tal *** x=22.923729 > 5 ***, y=38.796391, z=-17.018944 Why it will have an error related to Left_Caudate? Is the FreeSurferColorLut.txt file called somewhere ? Thanks! Guang _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469226/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cross-sectional analyis error
Hi, there, I am testing two subjects using cross-sectional FS. Both of they have being processed for almost four days. Both of them are stuck at the mris_fix_topology step, but there is no error message pops up. Subject#1 * INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ before topology correction, eno=-132 (nv=182824, nf=365912, ne=548868, g=67) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 71554 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 22 into 9 -merging segment 29 into 27 37 defects to be corrected 0 vertices coincident reading input surface /data1/radiology/m047599/subjects/027_S_0408_20060510/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9. (-4.6111) -vertex loglikelihood: -6.1352 (-3.0676) -normal dot loglikelihood: -3.5992 (-3.5992) -quad curv loglikelihood: -5.8849 (-2.9424) Total Loglikelihood : -24.8415 CORRECTING DEFECT 0 (vertices=30671, convex hull=1376) * Subject#2 * Correcting Topology of defect 2 with euler number 1 (0 loops) Nothing to correct for defect 2!! AFTER CORRECTION, EULER IS -262 Surface Diagnostics: eno=-262 (nv=157710, nf=315944, ne=473916) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces0 # of corner configurations 0 Correcting Topology of defect 3 with euler number -219 (110 loops) computing statistics for defect 3: 23911 vertices location: [ (168,58,111) - average intensity = 83.612 ] -gray ( 77.29 , 6.14 ) -white ( 93.87 , 3.59 ) -gray ( 79.92 , 20.78 ) -white ( 95.75 , 18.72 ) -intensity (77.286301 [log = -2.730186 ]- 93.865768 [log = -2.235836 ]) -curv (k1=-0.170 (0.615) , r1 = 5.894 | k2=-0.052 (0.142), r2 = 19.402 ) -curv (k1=-0.138 (0.656) , r1 = 7.230 | k2=-0.024 (0.219), r2 = 41.547 ) max face = 47468(47468) - loop = 1 (110) - ntries = [18,18997] BEST FITNESS (o)is -9.95545 mri =0.000 curv = 0.865 unmri = 6.496 ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 ) ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 ) BEST FITNESS (M) is 14.81362 mri =0.000 curv = 0.886 unmri = -18.358 ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 ) ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 ) Could any one tell me how to fix this problem, is there a method to ignore this fix_topology step? Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] convert vertex in tksurfer to point in tkmedit
Hello, there, I load lh.inflated of a subject using tksurfer, click a point (or vetex), then Click "Save Point") Meanwhile, I load the same subject in tkmedit, select "goto save point", I can see the saved point. If I try to convert multiple points (or vertices) from tksurfer to tkmedit, is there an equation? I guess I am looking for the equation which can convert Vertex RAS to Volume Index. Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] modification made to longitudinal results
Hi, there, I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use? recon-all -s subj.long.baseid or recon-all -long subj baseid Thanks! Guang _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to use time points
Hi, there, I have scans from two time points, and they have been cross-sectionally processed. But both of they missed some white matter in some slices, so I manually add control points to them, and re-run it. Both of them look fine now. Then, I send them to longitudinal stream. After the -base step is finished. I load the output in the based folder, those white matter are misclassified at the same place again. Is a method which can use the control points I added to the two time point when I called recon-all -base to build the base template. Or I need add control points to the built base subject again? Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] a question about FS longitudinal stream
Hi, there, I have a question about FS longitudinal stream, I have data from two time points which have been processed by FreeSurfer cross-sectional stream. I also built the base template using recon-all -base command, everything looks fine. When I ran the longitudinal stream, one of them stopped at the first step, it failed to do the skull stripping. I changed the watershed threshold, it works now. The question is, for this time point data, I want to use the following command line to finish the rest longitudinal analysis, recon-all -long tp_dat1 base_id -autorecon2 -autorecon3 Is it correct? Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer atlas and template
Hello, there, I have two questions about FreeSurfer default atlas and template, Will Freesurfer team build an atlas or template using 3T scans in future? Will Freesurfer team build an atlas or template using patients with disease in future? Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/___ 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.
Re: [Freesurfer] modification made to longitudinal results
Hello, Martin, Thanks a lot for your reply, but I am still not very clear about few issues. I think that is because of my unclear description. What happen is: I have two scans which I want to do longitudinal analysis, however, when I finish the cross-sectional analysis, I found the results are not so good because of the low contrast between white matter and gray matter. I added control points to these two scans, rerun them. The results looks much better now, then I go to the longitudinal stream. However, when I load the longitudinal results, I found the kind of problem happens again (lots of no-label region in superior frontal). So I added control points to the longitudinal results directly, and I want rerun them. Based on your reply, I need consider those longitudinal results which I added control points to as new timepoints, rerun them cross-sectionally again, is it correct? Thanks! Guang Here, I just want to add some control points to the FreeSurfer longitudinal results, not new time points. > Subject: Re: [Freesurfer] modification made to longitudinal results > From: mreu...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Date: Thu, 25 Feb 2010 10:33:36 -0500 > > Hi Guang, > > Depending on what you do you can choose different routes. Note, for both > of these you first need to run the new timepoint cross sectionally (step > 1 in the description > http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): > recon-all -all -s newtpid -i path/to/dicom > > Here are the two options once the cross sectional results are there: > > 1. you have only very few timepoints in the base/template so far (2 or > 3). In those cases I would recommend to rerun the base and rerun all the > longitudinals with the new and more accurate base. The commands are on > the Wiki and are the same as usual. > > 2. you have many time points in your base, the additional time point is > not likely to change the base much. In that case you can simply 'patch' > the base without reprocessing and only run a single longitudinal run. > > Let me know if you want to go route 2 because I am writing a script to > patch the base (there are a few files that need to be added so that the > longitudinal run will go through). If there is demand, I will put > priority on this and make it available. > > Best, Martin > > On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote: > > Hi, there, > > > > I need add some control points to the longitudinal results. > > After adding control points, I need rerun it. which command should I > > use? > > > > recon-all -s subj.long.baseid > > or > > recon-all -long subj baseid > > > > > > Thanks! > > Guang > > > > > > __ > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up > > now. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/___ 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] recon-all fails because of mri_label error
Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.0 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_3___ 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.
Re: [Freesurfer] recon-all fails because of mri_label error
I use v4.5.0, I also downloaded the new version of mri_label and tried it, but I got another error says that " mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/m047599/freesurfer-install/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz /home/m047599/freesurfer-install/freesurfer/bin/mri_ca_label: Permission denied." Thanks! Guang From: fis...@nmr.mgh.harvard.edu To: freesurfer...@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error What version are you running? On Mar 13, 2010, at 4:22 PM, Guang Zeng wrote: Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.0 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_3___ 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.
Re: [Freesurfer] recon-all fails because of mri_label error
Hello, Bruce, I loaded the brainmask.mgz, it has a bad skull-stripping results with cerebellum attached. I tried to fix this problem by adjusting the watershed parameters, but the interesting thing is: this is the base template subject which is created by the command line recon-all -base base_id -tp subj1 -tp subj2 -all I am not sure what is next command line I need to use after I fix the skull-stripping problem, recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 or recon-all -s base_id -autorecon2 Thanks! Guang From: fis...@nmr.mgh.harvard.edu To: freesurfer...@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error What version are you running? On Mar 13, 2010, at 4:22 PM, Guang Zeng wrote: Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.0 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850552/direct/01/___ 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] a question about wmparc.stats and aseg.stats
Hi, there, I have a question about wmparc.stats and aseg.stats, In aseg.stats, I read, # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1132816.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1156812, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1156812.00, mm^3 In wmparc.stats, I read # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 206821.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 244540, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 244540.00, mm^3 Why the BrainSegVolNotVent and BrainSegVol are so small in wmparc.stats? Those values in wmparc.stats are the sum of what? If I want to get the correct Brain Segmentation Volume Without Ventricles, which value I should use? the one from wmparc.stats or the one from aseg.stats? Thanks! Guang _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2___ 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] the thickness of manually selected vertex
Hi, there, I have two questions about the ?h.thickness file. If I load a subject's surface ?h.inflated using tksurfer, then I load its thickness file ?h.thickness, By clicking mouse on the surface, I can read the corresponding curvature value of a specific vertex. Q1, Here, the value next to 'Curvature' is actually its thickness value, right? Q2, If I select four vertexes on the surface, is there a way that I can save the thickness values of these four vertexes into a txt file? Thanks! Guang _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2___ 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.
Re: [Freesurfer] the thickness of manually selected vertex
Hello, Bruce, Thanks a lot! I think my new question is how to save a label file of the 4 vertices I selected. Thanks! Guang > Date: Wed, 24 Mar 2010 16:15:35 -0400 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] the thickness of manually selected vertex > > Q1: yes. > Q2: do you want each of them individually or the average? You can save a > label file of the 4 vertices and use mris_anatomical_stats to get the > average > > cheers > Bruce > > On Wed, 24 Mar 2010, Guang Zeng wrote: > > > > > Hi, there, > > > > I have two questions about the ?h.thickness file. > > > > If I load a subject's surface ?h.inflated using tksurfer, then I load its > > thickness file ?h.thickness, > > > > By clicking mouse on the surface, I can read the corresponding curvature > > value of a specific vertex. > > > > Q1, Here, the value next to 'Curvature' is actually its thickness value, > > right? > > Q2, If I select four vertexes on the surface, is there a way that I can > > save the thickness values of these four vertexes into a txt file? > > > > > > Thanks! > > Guang > > > > _ > > Hotmail is redefining busy with tools for the New Busy. Get more from your > > inbox. > > http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2 > > > 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. > _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_1___ 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.
Re: [Freesurfer] the thickness of manually selected vertex
Do I need convert the .label file to an annotation file before I run mris_anatomical_stats? Could I get the same results if I do something like this: 1. create the label file, and load it using MATLAB, 2. find the corresponding ID of vertices I clicked. 3. load .thickness file using matlab 4. find the corresponding thickness value of these vertice 5. compute the mean Thanks! Thank! Guang > Date: Wed, 24 Mar 2010 16:15:35 -0400 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] the thickness of manually selected vertex > > Q1: yes. > Q2: do you want each of them individually or the average? You can save a > label file of the 4 vertices and use mris_anatomical_stats to get the > average > > cheers > Bruce > > On Wed, 24 Mar 2010, Guang Zeng wrote: > > > > > Hi, there, > > > > I have two questions about the ?h.thickness file. > > > > If I load a subject's surface ?h.inflated using tksurfer, then I load its > > thickness file ?h.thickness, > > > > By clicking mouse on the surface, I can read the corresponding curvature > > value of a specific vertex. > > > > Q1, Here, the value next to 'Curvature' is actually its thickness value, > > right? > > Q2, If I select four vertexes on the surface, is there a way that I can > > save the thickness values of these four vertexes into a txt file? > > > > > > Thanks! > > Guang > > > > _ > > Hotmail is redefining busy with tools for the New Busy. Get more from your > > inbox. > > http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2 > ___ > 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. > _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850552/direct/01/___ 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.
