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 #-------------------------------------------- #@# 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 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 #-------------------------------------------- #@# 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 nschmans@W0084482(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 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 [michellevoss@cronos.vp.uiuc.edu:/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 [michellevoss@cronos.vp.uiuc.edu:/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 [michellevoss@cronos.vp.uiuc.edu:/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 [michellevoss@cronos.vp.uiuc.edu:/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 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 #-------------------------------------------- #@# 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 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