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