Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

can't change common-space subject in qdec
by Danielian, Laura (NIH/NINDS) [E] 25 Feb '10

25 Feb '10

Hi, I've created an average brain and would like to use that as the "common-space subject" in my qdec analysis. However, the program does not seem to allow editing of that box - I can't seem to delete or type over the default fsaverage. Is there a trick to changing this information or another way to load it at the command line? Thanks in advance for your help, Laura

2 1

LGN label or ROI....
by Ritobrato Datta 25 Feb '10

25 Feb '10

Hi All, Is there a method for obtaining an ROI for the lateral geniculate nucleus in freesurfer ? Thanks, Ri

3 2

correction of pial surface...
by Gonzalo Rojas 24 Feb '10

24 Feb '10

Hi: How can I correct the pial surface in the image that I am sending attached ?... Sincerely, -- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 4

QDEC covariate question
by lordowen 24 Feb '10

24 Feb '10

Dear freesurfer experts: We are using freesurfer to preform a cortical thickness analysis between patients and controls. We plan to use the mean_thickness and subject age as covariates. It's fine to analysis as group x age or group x mean_thickness, respectively. But when we set design as group x age x mean_thickness, an error report appeared in the terminal: -------- Matrix condition is 11355.6 ERROR: matrix is ill-conditioned or bad scaled, condno = 11355.6 Possible problem with experimental design: Check for duplicate entries and /or lack of range of continuous variables within a class. (continuous with values in Xg.dat) ------ Does the problem course by the different "range" from age value (between 18-28) and mean_thickness (between 2-4) with in the same subject? if so, how can we solve it? Does proportional scaling on age or mean_thickness help? Any comments are welcome and very appreciate. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Student Laboratory of Integrated Brain Research Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

2 3

mkanalysis-sess
by Samantha Clark 24 Feb '10

24 Feb '10

Hi, I have a question regarding creating a paradigm file and the command mkanalysis-sess. I am trying to analyze resting state data and wanted to know what the contents of the paradigm file should be. Also what would my mkanalysis-sess command be? Not sure what the -designtype and other options would be in this case. Can you please help? Thanks, Samantha

2 1

nmr-std-env error on seychelles
by Maximilien Chaumon 24 Feb '10

24 Feb '10

Hi Freesurfers, I have an issue with a job I launch on seychelles. I get this error message: /usr/local/freesurfer/nmr-std-env: line 98: syntax error near unexpected token `(' /usr/local/freesurfer/nmr-std-env: line 98: ` set path = ( /usr/pubsw/bin $path )' /var/spool/PBS/mom_priv/jobs/1258634.sey.SC: line 13: isxconcat-sess: command not found Since this is not a file I edited myself, I wonder what's wrong... Thanks, Max

2 1

convert vertex in tksurfer to point in tkmedit
by Guang Zeng 23 Feb '10

23 Feb '10

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/

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Re: [Freesurfer] recon-all doesn't recon-all
by Janani Dhinakaran 23 Feb '10

23 Feb '10

Thank you for your help. It again only ran for a minute. The difference this time seemed to be that it asked me to rerun the command with -force. I wrote out s0964091@CRIC-0012:~$ SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM to start with. Then I typed out what you sent s0964091@CRIC-0012:~$ recon-all -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 ERROR: /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 exists, delete or re-run with -force So I added -force to the beginning which caused an error- s0964091@CRIC-0012:~$ -force recon-all -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 No command '-force' found, did you mean: Command 'zforce' from package 'gzip' (main) -force: command not found I tried adding it in the end and as I said earlier, it ran well but only for a minute. It seems to have done mri_convert ans done a run1 and 3 without a run2 s0964091@CRIC-0012:~$ recon-all -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm -i /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 -force INFO: /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 s0964091 s0964091 39914 Feb 23 12:28 /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/scripts/recon-all.log Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm... Getting Series No INFO: Found 751 files in /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM INFO: Scanning for Series Number 2 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (512 512 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName Dhinakaran^Janani^ Date and time StudyDate 20100126 StudyTime 141335.671000 SeriesTime 142623.875000 AcqTime 142155.855000 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_ns_sag_p2_iso PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.48 InversionTime 900 RepetitionTime 1900 PhEncFOV 250 ReadoutFOV 250 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 90.3776 114.4676 105.9606 VolRes 0.4883 0.4883 1.0000 VolDim 512 512 176 Vc -0.0244 -0.9997 -0.0000 Vr -0.0170 0.0004 -0.9999 Vs -0.9996 0.0244 0.0170 VolCenter -2.7567 -8.2942 -17.5285 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=1900.00, TE=2.48, TI=900.00, flip angle=9.00 i_ras = (-0.0244253, -0.999702, -2.75516e-09) j_ras = (-0.0169601, 0.000414383, -0.999856) k_ras = (-0.999558, 0.0244218, 0.0169652) writing to /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/001.mgz... /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001 mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz mri_convert /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm... Getting Series No INFO: Found 751 files in /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM INFO: Scanning for Series Number 4 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 3 INFO: sorting. INFO: (512 512 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName Dhinakaran^Janani^ Date and time StudyDate 20100126 StudyTime 141335.671000 SeriesTime 144205.640000 AcqTime 143536.830000 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_ns_sag_p2_iso PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.64 InversionTime 900 RepetitionTime 1900 PhEncFOV 192 ReadoutFOV 192 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 72.1091 90.1873 96.0943 VolRes 0.3750 0.3750 0.8000 VolDim 512 512 176 Vc -0.0244 -0.9997 -0.0000 Vr -0.0170 0.0004 -0.9999 Vs -0.9996 0.0244 0.0170 VolCenter -2.2327 -4.0250 1.3025 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=1900.00, TE=2.64, TI=900.00, flip angle=9.00 i_ras = (-0.0244253, -0.999702, -2.75516e-09) j_ras = (-0.0169601, 0.000414383, -0.999856) k_ras = (-0.999558, 0.0244218, 0.0169652) writing to /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/subj001/mri/orig/002.mgz... #------------------------------------------ recon-all finished without error at Tue Feb 23 12:33:27 GMT 2010 done I'm quite perplexed now as to why it is going wrong. Is it possible at all that my data is not suitable for Freesurfer? Thanks for your time, Jan On 23 February 2010 09:00, Xue, Feng <xfgavin(a)gmail.com> wrote: > On Tue, Feb 23, 2010 at 12:27 AM, Janani Dhinakaran > <janinthesky(a)gmail.com> wrote: > > When I set SUBJECTS_DIR to /Desktop/..... I get this > > > > s0964091@CRIC-0012:~$ export > > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > > > Which makes it part of home anyway. > > > > When I add home into the path I get a double- > > > > s0964091@CRIC-0012:~$ export > > > SUBJECTS_DIR=~/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR > > > /home/s0964091/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > > > And the Recon-all has errors too. > > > > s0964091@CRIC-0012:~$ recon-all -i > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > > -i > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.d > here should be .dcm, meanwhile, you > don't need to export SUBJECTS_DIR, because we don't need global level > environment variables. > please try as below: > under your shell indicator, type: > > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > recon-all -i > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > -i > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > -s subj001 > > Hope this could solve your trouble. > > > ERROR: cannot find > > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.d > > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > > 2010 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Mon Feb 22 16:24:46 GMT 2010 > > > > > > It doesn't run recon at all. Unlike the previous command which did but > > incompletely. > > > > Jan > > > > > > On 22 February 2010 16:21, Xue, Feng <xfgavin(a)gmail.com> wrote: > >> > >> It seems that your problem is the recon-all script couldn't find your > >> SUBJECTS_DIR, possibly because you didn't give it full path. So I > >> suggest to try define SUBJECTS_DIR as > >> > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM, > >> then rerun your recon-all command as before. > >> > >> On Mon, Feb 22, 2010 at 10:44 PM, Janani Dhinakaran > >> <janinthesky(a)gmail.com> wrote: > >> > Is this what you meant: > >> > > >> > First I tried > >> > s0964091@CRIC-0012:~$ recon-all > >> > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> > ERROR: Flag > >> > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> > unrecognized. > >> > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 > UTC > >> > 2010 x86_64 GNU/Linux > >> > > >> > recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010 > >> > > >> > Then I tried putting full path in front of both file sets > >> > > >> > > >> > s0964091@CRIC-0012:~$ recon-all -i > >> > > >> > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > >> > -i > >> > > >> > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > >> > -s subj001 > >> > ERROR: cannot find > >> > > >> > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > >> > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 > UTC > >> > 2010 x86_64 GNU/Linux > >> > > >> > recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010 > >> > > >> > Jan > >> > > >> > > >> > On 22 February 2010 14:30, Xue, Feng <xfgavin(a)gmail.com> wrote: > >> >> > >> >> Try with full path, e.g. > >> >> > >> >> > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> >> > >> >> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran > >> >> <janinthesky(a)gmail.com> wrote: > >> >> > Hello, > >> >> > I ran recon-all on Friday. It ran for around a minute instead of > >> >> > 30-48 > >> >> > hours. Unfortunately, when I try tkmedit and other such commands, > the > >> >> > pictures don't visualise. > >> >> > So today I first confirmed that the SUBJECTS_DIR was in Desktop > path. > >> >> > (Because over the weekend it had gone back to usr/local... path and > >> >> > so I > >> >> > re-exported it just now.) > >> >> > Then I tried running recon-all again. > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > s0964091@CRIC-0012 > :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > >> >> > echo $SUBJECTS_DIR > >> >> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > >> >> > > >> >> > > >> >> > s0964091@CRIC-0012 > :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ > >> >> > recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i > >> >> > Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 > >> >> > ERROR: SUBJECTS_DIR > >> >> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not > >> >> > exist. > >> >> > > >> >> > Can anyone help me understand what I can do? > >> >> > Thanks > >> >> > Jan > >> >> > -- > >> >> > I am the Sun, I know no darkness. > >> >> > > >> >> > _______________________________________________ > >> >> > Freesurfer mailing list > >> >> > Freesurfer(a)nmr.mgh.harvard.edu > >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> >> > > >> >> > >> >> > >> >> > >> >> -- > >> >> Best Regards > >> >> > >> >> Xue, Feng Phd. candidate > >> >> Major in Developmental Cognitive Neuroscience > >> >> > >> >> National Key Laboratory of Cognitive Neuroscience and Learning > >> >> Beijing Normal University > >> >> Beijing, China. 100875 > >> >> Tel: +86-13810154455 > >> >> web: http://psychbrain.bnu.edu.cn > >> >> ============================================== > >> >> Welcome to MuDuo JinSheng BBS @ Beijing Normal University > >> >> telnet://bbs.mdjs.org > >> >> http://bbs.mdjs.org > >> > > >> > > >> > > >> > -- > >> > I am the Sun, I know no darkness. > >> > > >> > >> > >> > >> -- > >> Best Regards > >> > >> Xue, Feng Phd. candidate > >> Major in Developmental Cognitive Neuroscience > >> > >> National Key Laboratory of Cognitive Neuroscience and Learning > >> Beijing Normal University > >> Beijing, China. 100875 > >> Tel: +86-13810154455 > >> web: http://psychbrain.bnu.edu.cn > >> ============================================== > >> Welcome to MuDuo JinSheng BBS @ Beijing Normal University > >> telnet://bbs.mdjs.org > >> http://bbs.mdjs.org > > > > > > > > -- > > I am the Sun, I know no darkness. > > > > > > -- > Best Regards > > Xue, Feng Phd. candidate > Major in Developmental Cognitive Neuroscience > > National Key Laboratory of Cognitive Neuroscience and Learning > Beijing Normal University > Beijing, China. 100875 > Tel: +86-13810154455 > web: http://psychbrain.bnu.edu.cn > ============================================== > Welcome to MuDuo JinSheng BBS @ Beijing Normal University > telnet://bbs.mdjs.org > http://bbs.mdjs.org > -- I am the Sun, I know no darkness.

2 2

Troubleshooting incorrect annotations (cortical parcellation)
by Samuel Inverso 22 Feb '10

22 Feb '10

Hi All, It looks like the annotations are incorrect here, with the Parieto-occipital fissure annotated as the calcarine fissure on the attached surfaces. (Possibly because the occipital cortex seems to be squashed downwards?) The annotations are aparc.a2009s If that's, correct is there a method to fix the annotations? Thank you in advance for any help. Best regards, -Sam

2 1

Error during Fix Topology
by Joonkoo Park 22 Feb '10

22 Feb '10

Dear FreeSurfers, I got an error during Fix Topology step (seems like from the right hemisphere) in the recon-all process (see below for more information). I searched the ListServ and learned from other email threads that this may be due to incorrect segmentation of WM or Cerebellum, or possibly from skull stripping. I tried to follow the tutorial on manually fixing topological defects (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect) However, I wasn't sure what to look for because my current result does not yet have rh.white which allows to view WM segmentation in tkmedit window (or am I right?). What shall I do at this point? I'm very new to FreeSurfer, so it'd be great if anyone can give me some step-by-step approaches to troubleshoot this. Thanks. Joon ##### RELEVANT ERROR MESSAGE ###### #@# Fix Topology rh Sun Feb 21 12:55:08 EST 2010 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /net/raid/FSsubjdir/f06/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 f06 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* 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=-198 (nv=92924, nf=186244, ne=279366, g=100) 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 10 iterations marking ambiguous vertices... 46227 ambiguous faces found in tessellation segmenting defects... 82 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 66 into 61 -merging segment 75 into 73 80 defects to be corrected 0 vertices coincident reading input surface /net/raid/FSsubjdir/f06/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -7.8224 (-3.9112) -vertex loglikelihood: -6.6098 (-3.3049) -normal dot loglikelihood: -3.5417 (-3.5417) -quad curv loglikelihood: -5.7498 (-2.8749) Total Loglikelihood : -23.7237 CORRECTING DEFECT 0 (vertices=1720, convex hull=297) After retessellation of defect 0, euler #=-75 (68065,200835,132695) : difference with theory (-77) = -2 CORRECTING DEFECT 1 (vertices=103, convex hull=30) After retessellation of defect 1, euler #=-74 (68071,200866,132721) : difference with theory (-76) = -2 CORRECTING DEFECT 2 (vertices=282, convex hull=188) After retessellation of defect 2, euler #=-73 (68153,201199,132973) : difference with theory (-75) = -2 CORRECTING DEFECT 3 (vertices=19, convex hull=22) After retessellation of defect 3, euler #=-72 (68155,201211,132984) : difference with theory (-74) = -2 CORRECTING DEFECT 4 (vertices=775, convex hull=174) After retessellation of defect 4, euler #=-71 (68194,201406,133141) : difference with theory (-73) = -2 CORRECTING DEFECT 5 (vertices=40, convex hull=28) After retessellation of defect 5, euler #=-70 (68197,201426,133159) : difference with theory (-72) = -2 CORRECTING DEFECT 6 (vertices=30, convex hull=83) After retessellation of defect 6, euler #=-69 (68211,201499,133219) : difference with theory (-71) = -2 CORRECTING DEFECT 7 (vertices=140, convex hull=98) After retessellation of defect 7, euler #=-68 (68225,201587,133294) : difference with theory (-70) = -2 CORRECTING DEFECT 8 (vertices=52, convex hull=67) After retessellation of defect 8, euler #=-67 (68245,201674,133362) : difference with theory (-69) = -2 CORRECTING DEFECT 9 (vertices=25, convex hull=60) After retessellation of defect 9, euler #=-66 (68258,201740,133416) : difference with theory (-68) = -2 CORRECTING DEFECT 10 (vertices=38, convex hull=25) After retessellation of defect 10, euler #=-65 (68261,201758,133432) : difference with theory (-67) = -2 CORRECTING DEFECT 11 (vertices=21, convex hull=28) After retessellation of defect 11, euler #=-64 (68265,201780,133451) : difference with theory (-66) = -2 CORRECTING DEFECT 12 (vertices=103, convex hull=112) After retessellation of defect 12, euler #=-63 (68314,201983,133606) : difference with theory (-65) = -2 CORRECTING DEFECT 13 (vertices=78, convex hull=78) After retessellation of defect 13, euler #=-62 (68346,202110,133702) : difference with theory (-64) = -2 CORRECTING DEFECT 14 (vertices=13, convex hull=20) After retessellation of defect 14, euler #=-61 (68347,202118,133710) : difference with theory (-63) = -2 CORRECTING DEFECT 15 (vertices=20, convex hull=39) After retessellation of defect 15, euler #=-60 (68359,202164,133745) : difference with theory (-62) = -2 CORRECTING DEFECT 16 (vertices=20, convex hull=28) After retessellation of defect 16, euler #=-59 (68360,202177,133758) : difference with theory (-61) = -2 CORRECTING DEFECT 17 (vertices=71, convex hull=37) After retessellation of defect 17, euler #=-58 (68363,202198,133777) : difference with theory (-60) = -2 CORRECTING DEFECT 18 (vertices=37, convex hull=24) After retessellation of defect 18, euler #=-57 (68367,202217,133793) : difference with theory (-59) = -2 CORRECTING DEFECT 19 (vertices=56, convex hull=89) After retessellation of defect 19, euler #=-56 (68376,202281,133849) : difference with theory (-58) = -2 CORRECTING DEFECT 20 (vertices=132, convex hull=25) After retessellation of defect 20, euler #=-55 (68385,202313,133873) : difference with theory (-57) = -2 CORRECTING DEFECT 21 (vertices=90, convex hull=37) After retessellation of defect 21, euler #=-54 (68392,202347,133901) : difference with theory (-56) = -2 CORRECTING DEFECT 22 (vertices=432, convex hull=137) After retessellation of defect 22, euler #=-53 (68486,202692,134153) : difference with theory (-55) = -2 CORRECTING DEFECT 23 (vertices=505, convex hull=86) After retessellation of defect 23, euler #=-52 (68512,202807,134243) : difference with theory (-54) = -2 CORRECTING DEFECT 24 (vertices=479, convex hull=166) After retessellation of defect 24, euler #=-51 (68584,203106,134471) : difference with theory (-53) = -2 CORRECTING DEFECT 25 (vertices=531, convex hull=71) After retessellation of defect 25, euler #=-50 (68614,203224,134560) : difference with theory (-52) = -2 CORRECTING DEFECT 26 (vertices=12, convex hull=30) After retessellation of defect 26, euler #=-49 (68615,203234,134570) : difference with theory (-51) = -2 CORRECTING DEFECT 27 (vertices=35, convex hull=29) After retessellation of defect 27, euler #=-48 (68619,203253,134586) : difference with theory (-50) = -2 CORRECTING DEFECT 28 (vertices=32, convex hull=23) After retessellation of defect 28, euler #=-47 (68620,203263,134596) : difference with theory (-49) = -2 CORRECTING DEFECT 29 (vertices=39, convex hull=31) After retessellation of defect 29, euler #=-46 (68622,203285,134617) : difference with theory (-48) = -2 CORRECTING DEFECT 30 (vertices=8943, convex hull=1769) normal vector of length zero at vertex 73856 with 0 faces vertex 73856 has 0 face Numerical result out of range Linux ***** 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sun Feb 21 13:38:23 EST 2010

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