Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

how to svae FreeSurfer space?
by Guang Zeng 23 Jun '10

23 Jun '10

Hi, there, I have used FreeSurfer cross-sectional and longitudinal stream to process more than 1000 subjects, and the output file occupied almost all my storage space. Currently, I am thinking about delete some FreeSurfer output files to save some storage space, What I am think now is: 1. Delete some mgz files such as rawavg.mgz or orig.mgz which can be regenerate in a short time 2. Keep some files which need lots of time to regenerate such as talairach.m3z. But I am confused by the relationship and dependency of different output file at different stage, does anyone have suggestions? Thanks a lot! Guang _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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Re: [Freesurfer] question about clustering simulation
by Michael Waskom 23 Jun '10

23 Jun '10

Hi Doug, This looks very helpful! Should we use the fwhm size corresponding to the argument of the --fwhm flag when recon-all runs mri_surf2surf (for anatomical stats), or round the measure found in the fwhm.dat of the glmfit dir? Thanks, Mike ---------- Forwarded message ---------- From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: porterj(a)umn.edu Date: Tue, 27 Apr 2010 11:17:24 -0400 Subject: Re: [Freesurfer] question about clustering simulation Yea, that was a bug in the simulation program I used. I did confirm that the simulations were done on the correct hemisphere. Feel free to edit the files. I'll fix the master when I get a chance. doug James Porter wrote: > Doug- > > Let me be the first to say thank you for saving me massive amounts of > simulation time. One bug though: the right hemisphere files say they were > created using the left hemisphere, and mri_surfcluster rejects them. Would > it be verboten to just alter the csd files, or do you have versions that > were created off of fsaverage's right hemisphere? > > matacao:mult-comp-cor porterj$ head > fsaverage/rh/cortex/fwhm19/abs/th33/mc-z.csd > # simtype null-z > # anattype surface fsaverage lh > # FixGroupSubjectArea 1 > # merged 0 > # contrast NA > # seed 1271355821 > # thresh 3.300000 > # threshsign 0.000000 > # searchspace 74490.928733 > # nullfwhm 19.000000 > > Jim Porter, M.A. > Graduate Student > Clinical Science& Psychopathology Research > University of Minnesota > > > On 7/22/64 1:59 PM, Douglas N Greve wrote: > >> 1. Correct on both counts. When I wrote the simulation, I was only trying >> to replicate the random fields analysis. But with a simulation, you have >> more freedom that I am not yet exploiting. >> 2. This is what we are already doing with mc-z >> 3. I'm working on this as well. It turns out that the random fields >> approximation works a lot better when using the number of vertices. >> >> Also, I've run mc-z simulations under a bunch of thresholding and FWHM >> conditions for whole-hemisphere cortex labels. These will be integrated in >> new version of FS, but I've put them here >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor… well. There's a README file in there. This will make running your own >> time-consuming simulations unnecessary (when using the cortex mask at >> least). >> >> doug >> >> Anthony Dick wrote: >> >>> Hello all, >>> >>> I am interested in using the mri_glmfit simulation to control for >>> multiple comparisons in data I have run on the surface in AFNI. Before doing >>> this, I have a few questions: >>> >>> 1. What does the simulation with the mc-z flag do, exactly? It claims to >>> be comparable to AFNI's AlphaSim, but it takes a maximum cluster area for >>> each iteration, which is not exactly what AlphaSim does. Here is my guess: >>> >>> Given a surface, a given smoothness of the data, and a given per-vertex >>> threshold, for each iteration the simulation populates that surface with >>> random data taken from a normal distribution, thresholds the data, and >>> applies the smoothness of the actual data (supplied as an input parameter). >>> It then computes the maximum cluster size in area for that "image". Doing >>> this n iterations gives a distribution of maximum cluster sizes that occur >>> for random data of a given smoothness, and taking cluster sizes above a >>> certain percentile rank controls for the FWE at a level equal to that >>> percentile rank (e.g., 95th% controls for FWE = .05). AlphaSim does >>> something similar, although instead of taking maximum cluster sizes at each >>> iteration it computes all given cluster sizes. AlphaSim also allows for >>> different cluster connectivity radius, but it seems Freesurfer computes only >>> for neighboring vertices. All in all, if this is correct, it seems like a >>> good implementation. >>> >>> 2. It is my understanding that one could bypass running the glm in >>> Freesurfer and only compute the simulation, as the simulation only needs >>> information about the surface, and the smoothness of the data (which are >>> supplied by the user). To do so, you have to "fake out" Freesurfer to bypass >>> glm, but that turns out to be pretty painless. >>> >>> 3. In a future distribution, is it possible to modify this procedure to >>> also output maximum cluster sizes in terms of number of nodes, rather than >>> area? >>> >>> Can you please let me know if I am mistaken in any of these assumptions? >>> Thanks in advance. >>> >>> Anthony >>> >>> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

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Error while loading shared libraries: libtiff.so.3
by Cindy Eckart 23 Jun '10

23 Jun '10

Dear FreeSurfers, I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a Linux Debian machine (for details see below). After running stable till the -autorecon3 step, the process was killed because the shared library libtiff.so.3 was not found in this distribution. We currently try to fix this problem with a soft link from libtiff.so.4 (and hope that this will suffice to fix the problem) but notwithstanding wanted to ask if there are plans to adapt the FreeSurfer packages to the current libraries to circumvent that problem? Thank you very much for your help! Cindy My machine details: Linux membrane 2.6.26-2-amd64 #1 SMP Tue Mar 9 22:29:32 UTC 2010 x86_64 GNU/Linux Debian version 5.0.4 Shared library: GNU C Library stable release version 2.7, by Roland McGrath et al. Copyright (C) 2007 Free Software Foundation, Inc. Compiled by GNU CC version 4.3.2. Compiled on a Linux >>2.6.26-2-amd64<< system on 2010-01-14. Available extensions: crypt add-on version 2.1 by Michael Glad and others GNU Libidn by Simon Josefsson Native POSIX Threads Library by Ulrich Drepper et al BIND-8.2.3-T5B ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de

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Hemisphere matching problem during MC simulation
by Nick Schmansky 22 Jun '10

22 Jun '10

Dear Freesurfer experts, I have problems concerning the results of a MC simulation. When I checked the results with Qdec I discovered a matching problem for the right hemisphere. It seems like the used command runs the correct analyses for the right hemisphere, but fails projecting it properly to that one. It looks like freesurfer uses atlas and coordinates of the left hemisphere for the right hemisphere. I think the problem starts during MC simulation. Here's a "copy paste" entry of the *.log file, where I think freesurfer clearly mixes up hemisphere information: version $Id: mri_surfcluster.c,v 1.39.2.3 2009/01/15 01:06:01 greve Exp $ hemi = lh srcid = /home/hiwibp14/smb4k/CORTICAL/fmrt/Studie43/freesurfer/qdec/Untitled/rh-Avg-Intercept-thickness/sig.mgh For me obviously in the simulation process the programm mixes up information for right and left hemisphere during the analyses. This happens several times during analyses but only for analyses concerning the right hemisphere (see the complete attached log file). Is there any possibility to specify the command, adressing this problem like a special flag or something? Or is it possible to run the right hemisphere again separately? To run the simulation I used the following command line: mri_glmfit-sim \ --glmdir /home/hiwibp14/smb4k/CORTICAL/fmrt/Studie43/freesurfer/qdec/Untitled \ --sim mc-z 5000 1.3 mc-z.abs.1.3 \ --sim-sign abs \ --overwrite Thanks for your help and best regards, Johanna Feiler ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de

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bbregister with 4.5.0 fsfast
by ythomas 22 Jun '10

22 Jun '10

Hi, I have finished the 4.5.0 fsfast tutorial, and am wondering about the structure-function registration part. Currently, the tutorial recommends: fslregister-sess -s mgh-101.1. I notice that a single register.dat is produced. How are the multiple runs being handled now? Is only the first run used or all the runs are automatically used? I am asking because I would prefer to use bbregister. In bbregister, one passes to bbregister an anatomical subject id and a functional volume. So, (1) Which functional volume should I give to bbregister? (2) Are the functional volumes of the different runs co-registered after I run "preproc-sess"? (3) Presumably, I should also give bbregister the pre-smoothed, but motion corrected functional volume since smoothing would remove the gray-white boundary distinction that bbregister uses? Thanks, Thomas

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ASCII to MGH
by James Porter 21 Jun '10

21 Jun '10

Hello- I know how to use mri_convert and mris_convert to obtain ascii files of thickness values that I can read into stats software, but I'm having trouble going the other direction. Is there a good way to convert ascii lists of vertex values into mgh files so I can view them as overlays or utilize commands like mri_surfcluster? Thanks, Jim -- Jim Porter, M.A. Graduate Student Clinical Science& Psychopathology Research University of Minnesota

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error in running fsfast tutorial
by ythomas 21 Jun '10

21 Jun '10

Hi, I am trying to run the fsfast tutorial, and I am getting the following matlab error: Undefined function or method 'MRIwrite' for input arguments of type 'struct'. I ran the following commands: nexlin7:ythomas[test_fsfast/fsfast-tutorial/my-study] pwd /autofs/cluster/nexus/12/users/ythomas/data/test_fsfast/fsfast- tutorial/my-study nexlin7:ythomas[test_fsfast/fsfast-tutorial/my-study] preproc-sess -s mgh-101.1 -fwhm 6 I tried adding a startup.m file in /autofs/cluster/nexus/12/users/ ythomas/data/test_fsfast/fsfast-tutorial/my-study/startup.m before calling preproc-sess to tell matlab where to find MRIwrite, but that doesn't seem to help. Thanks, Thomas

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MatrixCopyRegion: bad source region error
by Guang Zeng 21 Jun '10

21 Jun '10

Hello, there, I am running the FreeSurfer Longitudinal stream at the recon-all -base step. Both of the time points were successfully processed, and the recon-all -base process failed at the first step (robust registration). I pasted the recon-all file below, can anyone help me to solve this problem? Thanks! Guang Mon Jun 21 11:23:53 CDT 2010 /data1/radiology/m047599/test3T_GW_New/018_S_0425_base /usr/local/biotools/freesurfer/freesurfer-v4.5.0/bin/recon-all -base 018_S_0425_base -tp 018_S_0425_20060619_160021_501 -tp 018_S_0425_20070615_092113_401 -all -force -notal-check -no-isrunning subjid 018_S_0425_base setenv SUBJECTS_DIR /data1/radiology/m047599/test3T_GW_New FREESURFER_HOME /usr/local/biotools/freesurfer/freesurfer-v4.5.0 Actual FREESURFER_HOME /home/biotools/freesurfer/freesurfer-v4.5.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux dnode49.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 cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 135168 total used free shared buffers cached Mem: 16508820 8186556 8322264 0 121040 6433072 -/+ buffers/cache: 1632444 14876376 Swap: 33554424 10532 33543892 ######################################## program versions used $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:53-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_watershed.cpp,v 1.67.2.5 2009/05/05 19:17:42 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_normalize.c,v 1.38.2.3 2009/08/02 15:00:46 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_register.c,v 1.63.2.3 2009/07/30 22:39:45 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_label.c,v 1.80.2.8 2009/07/30 23:22:53 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_concatenate_lta.c,v 1.3.2.1 2009/05/06 23:40:38 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.7 2009/06/08 23:45:06 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature_stats.c,v 1.28.2.5 2009/02/04 21:12:59 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_and.c,v 1.2.2.1 2009/05/22 00:58:19 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_or.c,v 1.1.2.1 2009/06/09 19:52:43 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/06/21-16:23:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fuse_segmentations.c,v 1.5.2.2 2009/06/10 19:42:00 nicks Exp $ User: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs ####################################### #-------------------------------------------- #@# Longitudinal Base Subject Creation Mon Jun 21 11:23:54 CDT 2010 /data1/radiology/m047599/test3T_GW_New/018_S_0425_base mri_robust_template --mov /data1/radiology/m047599/test3T_GW_New/018_S_0425_20060619_160021_501/mri/norm.mgz /data1/radiology/m047599/test3T_GW_New/018_S_0425_20070615_092113_401/mri/norm.mgz --lta /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/transforms/018_S_0425_20060619_160021_501_to_018_S_0425_base.lta /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/transforms/018_S_0425_20070615_092113_401_to_018_S_0425_base.lta --average 1 --template /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/norm_template.mgz $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ Using /data1/radiology/m047599/test3T_GW_New/018_S_0425_20060619_160021_501/mri/norm.mgz as movable/source volume. Using /data1/radiology/m047599/test3T_GW_New/018_S_0425_20070615_092113_401/mri/norm.mgz as movable/source volume. Using 2 input volumes Will output LTA transforms Using Method: 1 for template computation. Using /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/norm_template.mgz as template output volume. reading source '/data1/radiology/m047599/test3T_GW_New/018_S_0425_20060619_160021_501/mri/norm.mgz'... reading source '/data1/radiology/m047599/test3T_GW_New/018_S_0425_20070615_092113_401/mri/norm.mgz'... Registration::computeMultiresRegistration - Gaussian Pyramid - computing initial Transform -- using translation info Resolution: 4 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1685 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 12 ERR: 2.91623 weights average: 0.673008 zero: 0.272404 DONE - store transform -- old difference to prev. transform: 12.997 -- difference to prev. transform: 57.8691 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1705 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 6 ERR: 8.27977 weights average: 0.668251 zero: 0.263652 DONE - store transform -- old difference to prev. transform: 13.4697 -- difference to prev. transform: 53.1056 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1600 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 7 ERR: 12.9077 weights average: 0.68647 zero: 0.248436 DONE - store transform -- old difference to prev. transform: 12.7052 -- difference to prev. transform: 47.541 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1365 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 1.00415 weights average: 0.658358 zero: 0.304029 DONE - store transform -- old difference to prev. transform: 6.53516 -- difference to prev. transform: 16.4189 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1081 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 0.035687 weights average: 0.650796 zero: 0.321924 DONE - store transform -- old difference to prev. transform: 3.90493 -- difference to prev. transform: 10.8376 -- adjusting half-way maps Resolution: 3 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 5314 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 0.24948 weights average: 0.611185 zero: 0.359616 DONE - store transform -- old difference to prev. transform: 4.28862 -- difference to prev. transform: 6.43719 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 4294 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 8 ERR: 0.160071 weights average: 0.617197 zero: 0.352352 DONE - store transform -- old difference to prev. transform: 5.31445 -- difference to prev. transform: 9.87267 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 3378 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 7 ERR: 0.0633697 weights average: 0.604518 zero: 0.37093 DONE - store transform -- old difference to prev. transform: 4.12915 -- difference to prev. transform: 7.37041 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 2632 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 0.0562761 weights average: 0.605816 zero: 0.368541 DONE - store transform -- old difference to prev. transform: 4.26114 -- difference to prev. transform: 8.22338 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 2025 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 0.059443 weights average: 0.609209 zero: 0.364938 DONE - store transform -- old difference to prev. transform: 2.4914 -- difference to prev. transform: 7.55182 -- adjusting half-way maps Resolution: 2 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 9552 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 20.1679 weights average: 0.645418 zero: 0.305381 DONE - store transform -- old difference to prev. transform: 8.52965 -- difference to prev. transform: 13.3328 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 8126 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 16.9521 weights average: 0.639884 zero: 0.314177 DONE - store transform -- old difference to prev. transform: 7.61084 -- difference to prev. transform: 10.8168 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 6986 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 13.146 weights average: 0.638882 zero: 0.319353 DONE - store transform -- old difference to prev. transform: 4.06139 -- difference to prev. transform: 5.55399 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 5786 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 15 ERR: 8.50182 weights average: 0.63872 zero: 0.325268 DONE - store transform -- old difference to prev. transform: 4.50305 -- difference to prev. transform: 4.73783 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 4727 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 4 ERR: 6.22319 weights average: 0.641096 zero: 0.327269 DONE - store transform -- old difference to prev. transform: 6.68849 -- difference to prev. transform: 6.92671 -- adjusting half-way maps Resolution: 1 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 24663 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 4 ERR: 485.301 weights average: 0.787986 zero: 0.0833637 DONE - store transform -- old difference to prev. transform: 19.0035 -- difference to prev. transform: 11.5261 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 17729 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 241.516 weights average: 0.745962 zero: 0.155113 DONE - store transform -- old difference to prev. transform: 22.2147 -- difference to prev. transform: 12.4584 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 11871 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 53.4814 weights average: 0.693139 zero: 0.244882 DONE - store transform -- old difference to prev. transform: 16.0371 -- difference to prev. transform: 9.08422 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 8228 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 13.6448 weights average: 0.660016 zero: 0.293024 DONE - store transform -- old difference to prev. transform: 10.5501 -- difference to prev. transform: 6.29427 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 6097 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 5 ERR: 3.4466 weights average: 0.645146 zero: 0.318681 DONE - store transform -- old difference to prev. transform: 4.42548 -- difference to prev. transform: 3.9269 -- adjusting half-way maps Resolution: 0 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 35756 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 49.1283 weights average: 0.681103 zero: 0.261439 DONE - store transform -- old difference to prev. transform: 14.8937 -- difference to prev. transform: 7.19314 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 25635 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 14.8053 weights average: 0.671285 zero: 0.283909 DONE - store transform -- old difference to prev. transform: 9.43798 -- difference to prev. transform: 5.37094 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 19866 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 4.43877 weights average: 0.658105 zero: 0.301923 DONE - store transform -- old difference to prev. transform: 6.05639 -- difference to prev. transform: 4.00531 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 16099 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 1.55288 weights average: 0.652638 zero: 0.311572 DONE - store transform -- old difference to prev. transform: 5.05701 -- difference to prev. transform: 3.90321 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 0 non-zero voxels ) - compute robust estimate ( sat 4.685 )...MatrixCopyRegion: bad source region (1,1) --> (6,0) Linux dnode49.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 Mon Jun 21 11:31:36 CDT 2010 _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

2 1

Control point editing
by York, Philip 21 Jun '10

21 Jun '10

Hello, I have just edited 12 control points in the OFC/Gyrus rectus area of one of our subjects. I added 12 control points, all to regions of WM that were below 110 and I was very pleased with the output for that region once I ran -autorecon2-cp -autorecon3. However, this resulted in the temporal lobe on the same side to be almost completely neglected by the wm/pial surfaces. Areas that were originally considered WM (even though many areas were below 110 intensity) are now completely left out. What could be the cause of this? Am I changing the intensity threshold globally by editing the control points in one region? Thank you in advance, Philip

2 1

mni or tal to brodmann's
by Corey Keller 21 Jun '10

21 Jun '10

Hi freesurfers, I am wondering if there is a function in freesurfer to convert mni or talairach coordinates to brodmann's areas. I am hoping to input my RAS coordinates, transform them to either mni or talairach (which I know how to do), and then convert to and output the brodmann area. Thanks in advance. Best, Corey

2 1

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