Michelle, Which version of freesurfer is installed? I think the libg2c dependency was removed in the newest version.
Nick On Mon, 2008-08-18 at 11:28 -0500, Michelle W. Voss wrote: > Hello, > > This is my first time trying to use freesurfer on our data. We > collect siemens dicom images, so I first manually reconstructed > to .mgz format and tried running the recon-all script. I've posted > the log below. > > Any ideas for fix? > > thanks, > Michelle > > mri_convert -it siemens_dicom -ot mgz > ONR1_021508.MR.ONR_BASIC.23.1.2008.02.15.11.06.59.890625.162672170.IMA > 001.mgz > > > bash-3.2$ recon-all -s sub01 -autorecon-all > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects > Actual FREESURFER_HOME /Applications/freesurfer > Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun > 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 > #-------------------------------------------- > [EMAIL PROTECTED] MotionCor Mon Aug 18 08:43:20 CDT 2008 > Found 1 runs > /Applications/freesurfer/subjects/sub01/mri/orig/001.mgz > WARNING: only one run found. This is OK, but motion > correction cannot be performed on one run, so I'll > copy the run to rawavg and continue. > \n > cp /Applications/freesurfer/subjects/sub01/mri/orig/001.mgz > /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz \n > /Applications/freesurfer/subjects/sub01 > \n > mri_convert /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz > /Applications/freesurfer/subjects/sub01/mri/orig.mgz --conform \n > mri_convert /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz > /Applications/freesurfer/subjects/sub01/mri/orig.mgz --conform > $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt > from "1.146.2.2" claiming to beMailScanner warning: numerical links > are often malicious: 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > reading from /Applications/freesurfer/subjects/sub01/mri/rawavg.mgz... > TR=1800.00, TE=3.87, TI=900.00, flip angle=8.00 > i_ras = (-1, 2.02171e-10, 3.45578e-11) > j_ras = (-2.05103e-10, -0.985703, -0.168489) > k_ras = (-0, -0.168489, 0.985703) > Original Data has (1.33333, 1.33333, 1.3) mm size and (160, 192, 144) > voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from 4 to 0 (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /Applications/freesurfer/subjects/sub01/mri/orig.mgz... > \n mri_add_xform_to_header - > c /Applications/freesurfer/subjects/sub01/mri/transforms/talairach.xfm > /Applications/freesurfer/subjects/sub01/mri/orig.mgz > /Applications/freesurfer/subjects/sub01/mri/orig.mgz \n > INFO: extension is mgz > #-------------------------------------------- > [EMAIL PROTECTED] Nu Intensity Correction Mon Aug 18 08:43:33 CDT 2008 > \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 \n > /Applications/freesurfer/subjects/sub01/mri > /Applications/freesurfer/bin/mri_nu_correct.mni > --i orig.mgz --o nu.mgz --n 2 > nIters 2 > $Id: mri_nu_correct.mni,v 1.7 2007/01/06 00:01:14 nicks Exp $ > Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun > 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 > Mon Aug 18 08:43:33 CDT 2008 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] (i686- > apple-darwin8.8.1) on 2006-10-03 at 21:43:56 > tmpdir is ./tmp.mri_nu_correct.mni.14318 > /Applications/freesurfer/subjects/sub01/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14318/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14318/nu0.mnc > $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt > from "1.146.2.2" claiming to beMailScanner warning: numerical links > are often malicious: 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > reading from orig.mgz... > TR=1800.00, TE=3.87, TI=900.00, flip angle=8.00 > i_ras = (-1, 1.38778e-17, 3.46945e-18) > j_ras = (-3.46945e-18, 1.49012e-08, -1) > k_ras = (0, 1, 0) > writing to ./tmp.mri_nu_correct.mni.14318/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Mon Aug 18 08:43:39 CDT 2008 > nu_correct - > clobber ./tmp.mri_nu_correct.mni.14318/nu0.mnc > ./tmp.mri_nu_correct.mni.14318/nu1.mnc > [EMAIL PROTECTED]:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 > 08:43:39] running: > /Applications/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask - > nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp > -tmpdir /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/- > Tmp-/nu_correct_14368/ ./tmp.mri_nu_correct.mni.14318/nu0.mnc > ./tmp.mri_nu_correct.mni.14318/nu1.imp > > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Number of iterations: 50 > CV of field change: 0.00125843 > [EMAIL PROTECTED]:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 > 08:44:07] running: > /Applications/freesurfer/mni/bin/make_template -quiet -shrink > 3 ./tmp.mri_nu_correct.mni.14318/nu0.mnc > /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/-Tmp-/nu_correct_14368//template.mnc > > Transforming > slices:......................................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Transforming > slices:................................................................................................................................................................................................................................................................Done > > > -------------------------------------------------------- > Iteration 2 Mon Aug 18 08:44:10 CDT 2008 > nu_correct - > clobber ./tmp.mri_nu_correct.mni.14318/nu1.mnc > ./tmp.mri_nu_correct.mni.14318/nu2.mnc > [EMAIL PROTECTED]:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 > 08:44:10] running: > /Applications/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask - > nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp > -tmpdir /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/- > Tmp-/nu_correct_15024/ ./tmp.mri_nu_correct.mni.14318/nu1.mnc > ./tmp.mri_nu_correct.mni.14318/nu2.imp > > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Number of iterations: 2 > CV of field change: 0.000811469 > [EMAIL PROTECTED]:/Applications/freesurfer/subjects/sub01/mri/] [2008-08-18 > 08:44:12] running: > /Applications/freesurfer/mni/bin/make_template -quiet -shrink > 3 ./tmp.mri_nu_correct.mni.14318/nu1.mnc > /var/folders/VA/VAuuEIaYHGGfD8BbrnpkQE+++TI/-Tmp-/nu_correct_15024//template.mnc > > Transforming > slices:......................................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Not implemented yet in cache_volume_range_has_changed() > Transforming > slices:................................................................................................................................................................................................................................................................Done > > > > mri_convert ./tmp.mri_nu_correct.mni.14318/nu2.mnc nu.mgz --like > orig.mgz > mri_convert ./tmp.mri_nu_correct.mni.14318/nu2.mnc nu.mgz --like > orig.mgz > WARNING: --like does not work on multi-frame data > $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt > from "1.146.2.2" claiming to beMailScanner warning: numerical links > are often malicious: 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > reading from ./tmp.mri_nu_correct.mni.14318/nu2.mnc... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 1.38778e-17, 3.46945e-18) > j_ras = (-3.46945e-18, 1.49012e-08, -1) > k_ras = (0, 1, 0) > INFO: transform src into the like-volume: orig.mgz > writing to nu.mgz... > > > Mon Aug 18 08:44:24 CDT 2008 > mri_nu_correct.mni done > #-------------------------------------------- > [EMAIL PROTECTED] Talairach Mon Aug 18 08:44:24 CDT 2008 > /Applications/freesurfer/subjects/sub01/mri > \n talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm \n > /Applications/freesurfer/subjects/sub01/mri > /Applications/freesurfer/bin/talairach_avi > --i nu.mgz --xfm transforms/talairach.auto.xfm > $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ > Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun > 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 > Mon Aug 18 08:44:24 CDT 2008 > > -------------------------------------------- > > mri_convert nu.mgz talsrcimg.img > $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt > from "1.146.2.2" claiming to beMailScanner warning: numerical links > are often malicious: 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ > reading from nu.mgz... > TR=1800.00, TE=3.87, TI=900.00, flip angle=8.00 > i_ras = (-1, 1.38778e-17, 3.46945e-18) > j_ras = (-3.46945e-18, 1.49012e-08, -1) > k_ras = (0, 1, 0) > writing to talsrcimg.img... > Analyze Output Matrix > -1.000 -0.000 0.000 129.000; > 0.000 0.000 1.000 -131.394; > 0.000 -1.000 0.000 136.405; > 0.000 0.000 0.000 1.000; > -------------------- > INFO: set hdr.hist.orient to -1 > > -------------------------------------------- > > mpr2mni305 talsrcimg > Mon Aug 18 08:44:27 CDT 2008 > /Applications/freesurfer/bin/mpr2mni305 talsrcimg > $Id: mpr2mni305,v 1.3 2007/08/04 02:23:35 nicks Exp $ > target=711-2C_as_mni_average_305 > > --------------------------------------------------------------------- > analyzeto4dfp talsrcimg -O0 -y > --------------------------------------------------------------------- > > $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ > Mon Aug 18 08:44:28 2008 > Writing: talsrcimg.4dfp.hdr > $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ > Reading: talsrcimg.hdr > header size 348 bytes > hdr.dime.datatype offset=70 value=2 > hdr.dime.bitpix offset=72 value=8 > hdr.hist.orient offset=252 value=-1 > dimensionality 4 > dimensions 256 256 256 1 > Reading: talsrcimg.img > Writing: talsrcimg.4dfp.img > Writing: talsrcimg.4dfp.ifh > ifh2hdr talsrcimg -r0to255 > ori=2 > > --------------------------------------------------------------------- > gauss_4dfp talsrcimg 1.1 > --------------------------------------------------------------------- > > dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib > Referenced from: /Applications/freesurfer/bin/gauss_4dfp > Reason: image not found > Trace/BPT trap > ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 > ERROR: mpr2mni305 execution aborted > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log > Darwin cronos.vp.uiuc.edu 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun > 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 > > recon-all exited with ERRORS at Mon Aug 18 08:44:29 CDT 2008 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
