Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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.

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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

2 1

Imaging Center Director position at Ohio State
by Ruchika Prakash 22 Feb '10

22 Feb '10

Hi everyone: The Department of Psychology at The OHIO STATE UNIVERSITY seeks an outstanding scientist to serve as the inaugural director of a newly established College of Arts and Sciences Brain Imaging Center containing a state-of-the- art fMRI facility. The magnet (a Siemens Trio 3T) is housed in the psychology building but aims to serve a college-wide teaching and research mission. The position is expected to be filled at the full or associate professor level, but outstanding candidates at the advanced assistant level will also be considered. The individual would be expected to affiliate with and enhance one or more of the existing graduate training programs in the department (i.e., behavioral neuroscience, clinical, cognitive, developmental, quantitative, or social psychology). The individual is expected to have and maintain a strong funded research program involving fMRI and would be responsible for day-to-day operations of the imaging facility and its staff. Candidates are also expected to contribute to both graduate and undergraduate supervision and instruction. Interested individuals should submit a letter of application including a current CV, statement regarding specific qualifications and/or experience in running an fMRI facility, information about research and teaching interests, and three letters of recommendation. Materials should be addressed to: fMRI Director Search, Department of Psychology, Ohio State University, 1835 Neil Avenue, Columbus, OH 43210-1222. To ensure consideration, application materials must be received by March 15, 2010, but applications will be reviewed until the position is filled. For more information about the department, visit: www.psy.ohio-state.edu. Ohio State is an EEO/AA Employer. To build a diverse workforce, women, minorities, veterans, and individuals with disabilities are encouraged to apply. Sincerely, -Ruchika Prakash Ruchika Shaurya Prakash, Ph.D. Assistant Professor Department of Psychology Ohio State University Email: prakash.30(a)osu.edu Phone: (614) 292-8462 URL: http://faculty.psy.ohio-state.edu/prakash/lab/The_Lab.html

1 0

tkregister2 problems
by Sebastian Moeller 22 Feb '10

22 Feb '10

Dear Freesurfer Experts, I am a happy user of freesurfer for a number of years now. And finally I managed to switch over from v3.0.5 to 4.5.0. Most of this switch was pretty straightforward only slowed down by a few self-inflicted complications. One of the consequences of switching to V4 is that most of my functional 4D volumes now are floats instead of the short we used before. And regarding the floats, I just encountered a weird issue with tkregister2 (from freesufer-linux-centos4_x86_64-stable-pub-v4.5.0-full). I try to register 2 uncompressed single file nifti files, and the target does not appear only the moveable (when I hit the target button on the gui I just the image window turns black). Interestingly this also happens when I load the same volume as target and moveable: tkregister2 --regheader --reg tmp.reg --targ ./bold/003/f.nii --mov ./bold/003/f.nii -> nicely visible mov invisible targ, also fmo-targ does not help. however if I convert the file to int or short the targ becomes visible again: mri_convert -i /bold/003/f.nii -o /bold/003/fi.nii -odt int tkregister2 --regheader --reg tmp.reg --targ ./bold/003/fi.nii --mov ./bold/003/fi.nii -> nicely visible mov and targ, also: tkregister2 --regheader --reg tmp.reg --targ ./bold/003/fi.nii --mov ./bold/003/f.nii -> nicely visible mov and targ, but note: mri_convert -i /bold/003/fi.nii -o /bold/003/ff.nii -odt float tkregister2 --regheader --reg tmp.reg --targ ./bold/003/ff.nii --mov ./bold/003/ff.nii -> nicely visible mov invisible targ, So it looks like tkregister2 does not really like floats. Is there any thing I can do to work around this problem short of mri_converting all templates to temporary ints? I would be happy to help debug this issue, so please let me know what I can do to help. best regards & thanks for all the cool tools in freesurfer Sebastian -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

2 4

BrainSegVol in asegstats table
by Michael Waskom 22 Feb '10

22 Feb '10

Hi all, What is the definition of the "BrainSegVol" field when you print the segmentation stats to a table? It's smaller than just adding up all of the other fields in the table. Thanks! Best, Mike

2 1

mri_vol2surf resulting in different dimensions for two different images in the same space
by Joonkoo Park 22 Feb '10

22 Feb '10

Dear Surfers, I (successfully) resampled a functional data on the surface map using mri_vol2surf: > mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.func.mgh Then, I normalized this image to a standard space (fsaverage) using mri_surf2surf: > mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi lh The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 (identified from mri_info). This file can be opened from Matlab, and I can successfully get access to 163842 vertices. What I want now is to take the aparc+aseg information from the average brain (fsaverage) and be able identify which vertex falls under which ROI label. I decided to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to get label information at the dimension of 163842 x 1 x 1. So I ran: > mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi lh --o fsaverage/surf/lh.roi.mgh > mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi rh --o fsaverage/surf/rh.roi.mgh The resulting mgh files, however, had a dimension of 23406 x 1 x 7. 1. As I said, I wanted to get label information (roi number from the FreeSurferColorLUT) for each vertex of the surface image in the fsaverage space. Is this the right approach? And did I do this correctly (I'm concerned about many options above)? 2. If so, why is the resulting dimension different from the other one? I assume that it's probably a reshape issue, but how I can reshape the dimension to match 163842 x 1 x 1? Thanks in advance. Joon -- Joonkoo Park Ph.D. Candidate, Cognition & Cognitive Neuroscience Department of Psychology, University of Michigan

2 3

Re: [Freesurfer] recon-all doesn't recon-all
by Janani Dhinakaran 22 Feb '10

22 Feb '10

On 22 February 2010 16:27, 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 > 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. > -- I am the Sun, I know no darkness.

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Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 70
by Janani Dhinakaran 22 Feb '10

22 Feb '10

Thank you. I ran it correctly. It took less than a minute. Somethings not right. Here is a paste of everything past checking the SUBJECTS_DIR location with echo- s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ s0964091@CRIC-0012:~$ 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 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 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 Mon Feb 22 16:08:03 GMT 2010 done It didn't recon ALL. Anyone know what I'm doing wrong? Thanks Jan On 22 February 2010 15:48, Justin Ales <justin.ales(a)gmail.com> wrote: > I think you're missing the leading / in your full path > > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > should be: > > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > and the export line should be: > > export SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/ > > > SUBJECTS_DIR is the directory which contains ALL subjects _not_ the > current subject. > > > Justin Ales > > > From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> > To: Janani Dhinakaran <janinthesky(a)gmail.com> > Date: Mon, 22 Feb 2010 10:26:50 -0500 (EST) > Subject: Re: [Freesurfer] recon-all doesn't recon-all > > Hi Jan, > > Please try rerunning recon-all after removing the spaces or special > characters (if there are any) in the dicom files. > > Sita. > > > > On Mon, 22 Feb 2010, Janani Dhinakaran 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 Mon, Feb 22, 2010 at 7:36 AM, > <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > > Send Freesurfer mailing list submissions to > > freesurfer(a)nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-request(a)nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-owner(a)nmr.mgh.harvard.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Freesurfer digest..." > > > > Today's Topics: > > > > 1. recon-all doesn't recon-all (Janani Dhinakaran) > > 2. Re: recon-all doesn't recon-all (Janani Dhinakaran) > > 3. Difference between aparc+aseg and aparc.a2009s+aseg > > (Mohammed el Morabit) > > 4. Re: recon-all doesn't recon-all (Sita Kakunoori) > > 5. Re: mri_vol2surf resulting in different dimensions for two > > different images in the same space (Joonkoo Park) > > > > > > ---------- Forwarded message ---------- > > From: Janani Dhinakaran <janinthesky(a)gmail.com> > > To: freesurfer(a)nmr.mgh.harvard.edu > > Date: Mon, 22 Feb 2010 11:36:48 +0000 > > Subject: [Freesurfer] recon-all doesn't recon-all > > 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. > > > > > > ---------- Forwarded message ---------- > > From: Janani Dhinakaran <janinthesky(a)gmail.com> > > To: "Xue, Feng" <xfgavin(a)gmail.com>, freesurfer(a)nmr.mgh.harvard.edu > > Date: Mon, 22 Feb 2010 14:44:58 +0000 > > Subject: Re: [Freesurfer] recon-all doesn't recon-all > > 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. > > > > > > ---------- Forwarded message ---------- > > From: "Mohammed el Morabit" <M.elMorabit(a)student.TUDelft.NL> > > To: <freesurfer(a)nmr.mgh.harvard.edu> > > Date: Mon, 22 Feb 2010 16:05:53 +0100 > > Subject: [Freesurfer] Difference between aparc+aseg and aparc.a2009s+aseg > > > > Dear all, > > > > I am using freesurfer to generate a parcellation on the cortex. The > regions of this demarced cortex serve as ROIs in further research. My > question is... what is the difference between aparc+aseg and > aparc.a2009s+aseg? And which one should I use? > > > > Thanx in advance > > > > Morabit. > > > > ---------- Forwarded message ---------- > > From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> > > To: Janani Dhinakaran <janinthesky(a)gmail.com> > > Date: Mon, 22 Feb 2010 10:26:50 -0500 (EST) > > Subject: Re: [Freesurfer] recon-all doesn't recon-all > > > > Hi Jan, > > > > Please try rerunning recon-all after removing the spaces or special > characters (if there are any) in the dicom files. > > > > Sita. > > > > > > > > On Mon, 22 Feb 2010, Janani Dhinakaran 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 > >>> > >> > >> > >> > >> > > > > > > > > ---------- Forwarded message ---------- > > From: Joonkoo Park <joonkoo(a)umich.edu> > > To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > > Date: Mon, 22 Feb 2010 10:36:51 -0500 > > Subject: Re: [Freesurfer] mri_vol2surf resulting in different dimensions > for two different images in the same space > > Thanks Doug, > > > > Where can I find the surface annotation for the fsaverage (or any > > other template) data? > > I will need to import the data into matlab eventually, so I'm thinking > > that the surface annotation file should be readable using load_mgh.m > > (and writable using save_mgh.m). I'm very new to FreeSurfer so I'd > > really appreciate if you can describe each step for me. > > > > Thank you. > > > > Joon > > > > > > > > On Fri, Feb 19, 2010 at 11:47 AM, Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu> wrote: > >> You're better off loading in the surface annotation directly rather than > >> dealing with aparc+aseg. To make surf2surf output the right dimensions, > add > >> --noreshape. > >> > >> doug > >> > >> Joonkoo Park wrote: > >>> > >>> Dear Surfers, > >>> > >>> I (successfully) resampled a functional data on the surface map using > >>> mri_vol2surf: > >>> > >>> > >>>> > >>>> mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp > >>>> nearest --hemi lh --o lh.func.mgh > >>>> > >>> > >>> Then, I normalized this image to a standard space (fsaverage) using > >>> mri_surf2surf: > >>> > >>> > >>>> > >>>> mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval > >>>> sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi > lh > >>>> > >>> > >>> The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 > >>> (identified from mri_info). This file can be opened from Matlab, and I > >>> can successfully get access to 163842 vertices. What I want now is to > >>> take the aparc+aseg information from the average brain (fsaverage) and > >>> be able identify which vertex falls under which ROI label. I decided > >>> to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to > >>> get label information at the dimension of 163842 x 1 x 1. So I ran: > >>> > >>> > >>>> > >>>> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage > >>>> --projfrac 0.5 --interp nearest --hemi lh --o > fsaverage/surf/lh.roi.mgh > >>>> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage > >>>> --projfrac 0.5 --interp nearest --hemi rh --o > fsaverage/surf/rh.roi.mgh > >>>> > >>> > >>> The resulting mgh files, however, had a dimension of 23406 x 1 x 7. > >>> > >>> 1. As I said, I wanted to get label information (roi number from the > >>> FreeSurferColorLUT) for each vertex of the surface image in the > >>> fsaverage space. Is this the right approach? And did I do this > >>> correctly (I'm concerned about many options above)? > >>> > >>> 2. If so, why is the resulting dimension different from the other one? > >>> I assume that it's probably a reshape issue, but how I can reshape the > >>> dimension to match 163842 x 1 x 1? > >>> > >>> Thanks in advance. > >>> > >>> Joon > >>> > >>> -- > >>> Joonkoo Park > >>> Ph.D. Candidate, Cognition & Cognitive Neuroscience > >>> Department of Psychology, University of Michigan > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > >> -- > >> 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 > >> > >> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- I am the Sun, I know no darkness.

2 1

Difference between aparc+aseg and aparc.a2009s+aseg
by Mohammed el Morabit 22 Feb '10

22 Feb '10

Dear all, I am using freesurfer to generate a parcellation on the cortex. The regions of this demarced cortex serve as ROIs in further research. My question is... what is the difference between aparc+aseg and aparc.a2009s+aseg? And which one should I use? Thanx in advance Morabit.

2 1

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