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

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