Hi Richard, thanks for pointing this out – I’ll take a look into it.
best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Jones, Richard" richard.jones@choa.org Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Thursday, April 19, 2018 at 9:49 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305
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 nicks@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 [fsdev@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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 55 CV of field change: 0.000965325
mri_convert ./tmp.mri_nu_correct.mni.9696/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9696/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ 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