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.mgz / .mgh files created by mrtrix tools are not correctly read by FreeSurfer's tools #952

@ansk

Description

@ansk

Dear experts,
I found that the FreeSurfer tools are segfaulting when reading the .mgz / .mgh files created by mrtrix tools. I tested this on FreeSurfer 5.3 as well as on dev version of FreeSurfer from 2/2017. I am using most recent build of mrtrix on master branch: 0.3.15-522-gbc67f1a1

Example: orig.mgz is file created by freeSurfer.

mrconvert orig.mgz orig_mrtrix.mgz

mrinfo orig_mrtrix.mgz 
************************************************
Image:               "orig_mrtrix.mgz"
************************************************
  Dimensions:        256 x 256 x 256
  Voxel size:        1 x 1 x 1
  Data strides:      [ -1 3 -2 ]
  Format:            MGZ (compressed MGH)
  Data type:         unsigned 8 bit integer
  Intensity scaling: offset = 0, multiplier = 1
  Transform:                    1   -1.11e-16   4.657e-10      -131.2
                        5.551e-17           1   7.276e-12      -114.8
                       -4.657e-10  -7.276e-12           1      -101.7

mri_info orig_mrtrix.mgz 
Floating point exception

mri_convert orig_mrtrix.mgz orig_mrtrix2.mgz

mri_convert.bin orig_mrtrix.mgz orig_mrtrix2.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig_mrtrix.mgz...
/hydra-db/hydra_io/vypocty/skoch/bin/freesurfer_dev_20170208/bin/mri_convert: line 3: 11714 Segmentation fault      mri_convert.bin "$@"

mri_binarize --i orig_mrtrix.mgz --min 1 --max 255 --o orig_mrtrix_binarized.mgz --count junk.txt

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /hydradb/hydra_io/vypocty/freeSurfer/v6.1beta/CANEF/A_in_progress/skoch/ESO_P00007_20100611_1217_1_base/mri
cmdline mri_binarize.bin --i orig_mrtrix.mgz --min 1 --max 255 --o orig_mrtrix_binarized.mgz --count junk.txt 
sysname  Linux
hostname sup1.ad.nudz.cz
machine  x86_64
user     skoch

input      orig_mrtrix.mgz
frame      0
nErode3d   0
nErode2d   0
output     orig_mrtrix_binarized.mgz
Binarizing based on threshold
min        1
max        255
binval        1
binvalnot     0
/hydra-db/hydra_io/vypocty/skoch/bin/freesurfer_dev_20170208/bin/mri_binarize: line 3: 11922 Segmentation fault      mri_binarize.bin "$@"

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