How does the input image look, ie, orig.mgz?
On 04/19/2018 09:49 AM, Jones, Richard wrote: > > I ran the command shown below to do recon-all on DICOM images from a > Philips Ingenia scanner using the development version of freesurfer on > a Mac running high Sierra. > > recon-all -i > /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm -subject > HOPE_SS020 –all > > The program crashed with the error “ERROR: mpr2mni305 failed, see > transforms/talairach_avi.log” > > The talairach_avi.log file is shown below, followed by the log file. > As a test I ran the same command, on the same data, using Freesurfer 6 > and that ran without problems (except that it didn’t handle the > diffusion tags in the Philips DICOM header correctly so I had to set > FS_LOAD_DWI=0, this was not a problem in the development version). Any > suggestions as to what may be causing the problems with the library in > the development version? > > Thanks, > > Richard > > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri > > /Applications/freesurfer_dev/bin/talairach_avi > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ > > Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar > 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 > > Thu Apr 19 08:45:01 EDT 2018 > > mri_convert.bin orig_nu.mgz talsrcimg.img > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from orig_nu.mgz... > > TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 > > i_ras = (-1, 7.45058e-09, 0) > > j_ras = (3.72529e-09, -4.88944e-09, -1) > > k_ras = (0, 1, 4.88944e-09) > > writing to talsrcimg.img... > > Analyze Output Matrix > > -1.00000 0.00000 0.00000 128.15305; > > 0.00000 -0.00000 1.00000 -116.15433; > > 0.00000 -1.00000 0.00000 128.60870; > > 0.00000 0.00000 0.00000 1.00000; > > -------------------- > > INFO: set hdr.hist.orient to -1 > > mpr2mni305 talsrcimg > > Thu Apr 19 08:45:02 EDT 2018 > > /Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg > > $Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman 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 $ > > Thu Apr 19 08:45:02 2018 > > 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/opt/gcc/lib/gcc/7/libgfortran.4.dylib > > Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp > > Reason: image not found > > Abort > > ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134 > > ERROR: mpr2mni305 execution aborted > > Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499 > > Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499 > > INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects > > Actual FREESURFER_HOME /Applications/freesurfer_dev > > Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar > 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 > > /Applications/freesurfer_dev/subjects/HOPE_SS020 > > \n mri_convert > /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n > > mri_convert.bin > /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from > /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm... > > Starting DICOMRead2() > > dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm > > dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat > > Ref Series No = 301 > > Found 202 files, checking for dicoms > > Found 200 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: -0.897217 -0.0611658 0.0354633 > > Vs: -0.996909 -0.0679621 0.0394038 > > Second Sorting > > IsDWI = 0, IsPhilipsDWI = 0 > > Counting frames > > nframes = 1 > > nslices = 200 > > ndcmfiles = 200 > > PE Dir = ROW (dicom read) > > Loading pixel data > > TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 > > i_ras = (0.0644896, -0.994415, 0.0835493) > > j_ras = (0.0448617, -0.08075, -0.995724) > > k_ras = (0.996909, 0.0679621, 0.0394038) > > writing to > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz... > > #-------------------------------------------- > > #@# MotionCor Thu Apr 19 08:44:06 EDT 2018 > > Found 1 runs > > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz > > Checking for (invalid) multi-frame inputs... > > Only one run found so motion > > correction will not be performed. I'll > > copy the run to rawavg and continue. > > \n cp > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz \n > > /Applications/freesurfer_dev/subjects/HOPE_SS020 > > \n mri_convert > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz --conform \n > > mri_convert.bin > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz --conform > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz... > > TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 > > i_ras = (0.0644896, -0.994415, 0.0835493) > > j_ras = (0.0448617, -0.08075, -0.995724) > > k_ras = (0.996909, 0.0679621, 0.0394038) > > changing data type from short to uchar (noscale = 0)... > > MRIchangeType: Building histogram > > Reslicing using trilinear interpolation > > writing to > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz... > > \n mri_add_xform_to_header -c > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/transforms/talairach.xfm > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz \n > > INFO: extension is mgz > > #-------------------------------------------- > > #@# Talairach Thu Apr 19 08:44:12 EDT 2018 > > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri > > \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 > --proto-iters 1000 --distance 50 \n > > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri > > /Applications/freesurfer_dev/bin/mri_nu_correct.mni > > --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 > --distance 50 > > nIters 1 > > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ > > Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar > 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 > > Thu Apr 19 08:44:12 EDT 2018 > > Program nu_correct, built from: > > Package MNI N3, version 1.12.0, compiled by > ni...@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on > 2015-06-19 at 15:37:08 > > /usr/bin/bc > > tmpdir is ./tmp.mri_nu_correct.mni.9696 > > /Applications/freesurfer_dev/subjects/HOPE_SS020/mri > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9696/nu0.mnc -odt float > > mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9696/nu0.mnc -odt float > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from orig.mgz... > > TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 > > i_ras = (-1, 7.45058e-09, 0) > > j_ras = (3.72529e-09, -4.88944e-09, -1) > > k_ras = (0, 1, 4.88944e-09) > > changing data type from uchar to float (noscale = 0)... > > writing to ./tmp.mri_nu_correct.mni.9696/nu0.mnc... > > -------------------------------------------------------- > > Iteration 1 Thu Apr 19 08:44:14 EDT 2018 > > nu_correct -clobber ./tmp.mri_nu_correct.mni.9696/nu0.mnc > ./tmp.mri_nu_correct.mni.9696/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.9696/0/ -iterations 1000 -distance 50 > > [fs...@meshuga.choa.org:/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/] > > [2018-04-19 08:44:14] running: > > /Applications/freesurfer_dev/mni/bin/nu_estimate_np_and_em -parzen > -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 > -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute > -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9696/0/ > ./tmp.mri_nu_correct.mni.9696/nu0.mnc > ./tmp.mri_nu_correct.mni.9696/nu1.imp > > Processing:.................................................................Done > > Processing:.................................................................Done > > Processing:.................................................................Done > > 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reading from ./tmp.mri_nu_correct.mni.9696/nu1.mnc... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 7.45058e-09, 0) > > j_ras = (3.72529e-09, -4.88944e-09, -1) > > k_ras = (0, 1, 4.88944e-09) > > INFO: transform src into the like-volume: orig.mgz > > changing data type from float to uchar (noscale = 0)... > > MRIchangeType: Building histogram > > writing to orig_nu.mgz... > > Thu Apr 19 08:45:01 EDT 2018 > > mri_nu_correct.mni done > > \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n > > talairach_avi log file is transforms/talairach_avi.log... > > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log > > > > _______________________________________________ > 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 The 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