SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 143704 num faces : 287404 num strips : 0 surface area: 125661 AvgVtxArea 0.874440 AvgVtxDist 1.078393 StdVtxDist 0.419625 ctr : (0.000782013, 0.000278473, -0.000354767) vertex locs : surfaceRAS talairch.xfm: 1.055 0.061 0.112 -14.422; -0.160 1.180 0.231 -36.683; -0.122 -0.333 1.316 -37.246; 0.000 0.000 0.000 1.000; surfaceRAS to talaraiched surfaceRAS: 1.055 0.061 0.112 -0.656; -0.160 1.180 0.231 -13.306; -0.122 -0.333 1.316 -39.910; 0.000 0.000 0.000 1.000; talairached surfaceRAS to surfaceRAS: 0.930 -0.067 -0.068 -2.975; 0.104 0.800 -0.149 4.763; 0.113 0.196 0.716 31.244; 0.000 0.000 0.000 1.000; volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : (-0.0000, -0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : (11.4210, 20.5397, 4.2289) file : ../mri/filled-pretess255.mgz cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:20:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs s000_open_brain_sanlm_+TIR_normlalized lh ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:21:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:26:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:26:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:28:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2013/07/10-16:39:42-GMT sysname Linux hostname frioul03 machine x86_64 surfacefile s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 143704 nfaces 287404 total_area 125660.585938 group_avg_vtxarea_loaded 0 avgvtxarea 0.874440 avgvtxdist 1.078393 stdvtxdist 0.419625 vtx0xyz 30.075546 -90.141014 -31.145763
2013/7/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > and how about: > > mris_info s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere > > > On Wed, 10 Jul 2013, fatma zribi wrote: > > Dear Bruce, >> this is the result: >> >> -rwxrwxr-x 1 zribi.f scalp 5175759 Jun 21 14:57 >> s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere >> >> >> 2013/7/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Hi Fatma >> >> this not what we meant. From here please run: >> cd .. >> ls -l s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere >> >> cheers >> Bruce >> >> On Wed, 10 Jul 2013, fatma zribi wrote: >> >> >> >> ---------- Forwarded message ---------- >> From: fatma zribi <zribi.fa...@gmail.com> >> Date: 2013/7/10 >> Subject: Re: [Freesurfer] Fwd: how to use mris_register? >> To: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> >> >> Copie1/s000_open_brain_sanlm_+**TIR_normlalized$ ls -l >> total 704 >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 bem >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 label >> drwxrwxr-x 4 zribi.f scalp 4096 Jul 5 17:12 mri >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 9 10:44 scripts >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 SD >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 src >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 stats >> drwxrwxr-x 6 zribi.f scalp 4096 Jul 9 10:44 surf >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 tmp >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 touch >> drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 trash >> >> >> >> 2013/7/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> I meant can you run it and send us the results? If we >> can't open the file it is not an FS issue, >> but something with >> the file system. Run ls -l with the same path that you >> are giving mris_register >> >> Bruce >> >> >> On Wed, 10 Jul 2013, fatma zribi wrote: >> >> Hi Bruce, >> Yes i can run ls -l in the directory >> >> >> 2013/7/10 Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> Hi Fatma >> >> are you sure you don't have a typo in the >> path? Can you run ls -l on that file? >> Bruce >> On Wed, 10 Jul 2013, fatma zribi wrote: >> >> >> >> ---------- Forwarded message >> ---------- >> From: fatma zribi < >> zribi.fa...@gmail.com> >> Date: 2013/7/10 >> Subject: Re: [Freesurfer] how to use >> mris_register? >> To: Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> >> >> Hi Bruce, >> >> Thank you very much for your help but >> it still don't work. >> >> mris_register >> s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere >> avg_all_subjects_SD/lh.reg.**template.tif >> lh.sphere_reg >> >> $Id: mris_register.c,v 1.59 >> 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 >> 2011/04/27 19:21:05 nicks Exp $ >> reading surface from >> s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere... >> MRISread(s000_open_brain_** >> sanlm_+TIR_normlalized/surf/**lh.sphere): could not open >> file >> No such file or directory >> mris_register: could not read surface >> file >> s000_open_brain_sanlm_+TIR_** >> normlalized/surf/lh.sphere >> No such file or directory >> >> note that the file exist in the >> folder and i have changed the SUBJECT_DIR to the >> appropriate >> folder >> >> Thank you very much for your help >> >> with best regards, >> >> Fatma >> >> >> >> 2013/7/9 Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> Hi Fatma >> >> don't use the -1 flag if you >> are regtering to a template, only if you are >> registering >> individual >> surfaces to each >> other. You probably want the >> output to be named lh.sphere_reg and go in >> the s000/surf >> dir. >> >> cheers >> Bruce >> >> On Tue, 9 Jul 2013, fatma zribi >> wrote: >> >> Dear Mr, >> >> When I execute >> mris_register to register one subject to a template., >> I have this >> message of >> error: >> >> mris_register -1 >> s000/surf/lh.sphere >> avg_all_subjects_SD/lh.reg.**template.tif >> sphere_reg >> treating target as a >> single subject's surface... >> $Id: mris_register.c,v >> 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v >> 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> reading surface from >> s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere... >> MRISread(s000_open_brain_ >> **sanlm_+TIR_normlalized/surf/**lh.sphere): >> could not open >> file >> No such file or directory >> mris_register: could not >> read surface file s000/surf/lh.sphere >> No such file or directory >> >> note that the file exist >> in the specifeid SUBJECT_DIR >> >> Thank you for your help >> >> Fatma >> >> >> >> >> >> 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 <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. >> >> >> >> >> >> >> >> >> >> >> >>
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