There could be a bug here related to new FSL 6.0+ fslmaths behavior.  Please 
try modifying:

https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh

line 189 to:

${FSLDIR}/bin/fslmaths ${WD}/PhaseOne_mask_gdc -mas ${WD}/PhaseTwo_mask_gdc 
-ero -bin -Tmin ${WD}/Mask

Matt.

From: <hcp-users-boun...@humanconnectome.org> on behalf of Simon Wein 
<simon.w...@psychologie.uni-regensburg.de>
Date: Wednesday, May 22, 2019 at 8:28 AM
To: Timothy Coalson <tsc...@mst.edu>
Cc: Wilhelm Malloni <wilhelm.mall...@psychologie.uni-regensburg.de>, 
"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Error while running 
"GenericfMRIVolumeProcessingPipeline.sh"

Thank you very much for your suggestion.
We already use FSL 6.0.1 (and Freesurfer 6.0.0), sorry for my inaccuracy.
The output of "fslhd ${WD}/BothPhases" is:

filename    BothPhases.nii.gz
size of header    348
data_type    INT32
dim0        4
dim1        104
dim2        104
dim3        72
dim4        6
dim5        1
dim6        1
dim7        1
vox_units    mm
time_units    s
datatype    8
nbyper        4
bitpix        32
pixdim0        1.000000
pixdim1        2.000000
pixdim2        2.000000
pixdim3        2.000000
pixdim4        7.700000
pixdim5        0.000000
pixdim6        0.000000
pixdim7        0.000000
vox_offset    352
cal_max        0.000000
cal_min        0.000000
scl_slope    1.000000
scl_inter    0.000000
phase_dim    0
freq_dim    0
slice_dim    0
slice_name    Unknown
slice_code    0
slice_start    0
slice_end    0
slice_duration    0.000000
toffset        0.000000
intent        Unknown
intent_code    0
intent_name
intent_p1    0.000000
intent_p2    0.000000
intent_p3    0.000000
qform_name    Scanner Anat
qform_code    1
qto_xyz:1    -1.995593 0.092717 0.094922 93.702583
qto_xyz:2    -0.105543 -1.976261 -0.288537 118.937881
qto_xyz:3    0.080419 -0.292910 1.976799 -43.901993
qto_xyz:4    0.000000 0.000000 0.000000 1.000000
qform_xorient    Right-to-Left
qform_yorient    Anterior-to-Posterior
qform_zorient    Inferior-to-Superior
sform_name    Scanner Anat
sform_code    1
sto_xyz:1    -1.995594 0.092714 0.094922 93.702583
sto_xyz:2    -0.105540 -1.976261 -0.288537 118.937881
sto_xyz:3    0.080420 -0.292910 1.976799 -43.901993
sto_xyz:4    0.000000 0.000000 0.000000 1.000000
sform_xorient    Right-to-Left
sform_yorient    Anterior-to-Posterior
sform_zorient    Inferior-to-Superior
file_type    NIFTI-1+
file_code    1
descrip        6.0.1
aux_file


The output of "fslhd ${WD}/Mask.nii.gz" is:

filename    Mask.nii.gz
size of header    348
data_type    FLOAT32
dim0        4
dim1        104
dim2        104
dim3        72
dim4        3
dim5        1
dim6        1
dim7        1
vox_units    mm
time_units    s
datatype    16
nbyper        4
bitpix        32
pixdim0        1.000000
pixdim1        2.000000
pixdim2        2.000000
pixdim3        2.000000
pixdim4        7.700000
pixdim5        0.000000
pixdim6        0.000000
pixdim7        0.000000
vox_offset    352
cal_max        0.000000
cal_min        0.000000
scl_slope    1.000000
scl_inter    0.000000
phase_dim    0
freq_dim    0
slice_dim    0
slice_name    Unknown
slice_code    0
slice_start    0
slice_end    0
slice_duration    0.000000
toffset        0.000000
intent        Unknown
intent_code    0
intent_name
intent_p1    0.000000
intent_p2    0.000000
intent_p3    0.000000
qform_name    Scanner Anat
qform_code    1
qto_xyz:1    -1.995593 0.092717 0.094922 93.702583
qto_xyz:2    -0.105543 -1.976261 -0.288537 118.937881
qto_xyz:3    0.080419 -0.292910 1.976799 -43.901993
qto_xyz:4    0.000000 0.000000 0.000000 1.000000
qform_xorient    Right-to-Left
qform_yorient    Anterior-to-Posterior
qform_zorient    Inferior-to-Superior
sform_name    Scanner Anat
sform_code    1
sto_xyz:1    -1.995594 0.092714 0.094922 93.702583
sto_xyz:2    -0.105540 -1.976261 -0.288537 118.937881
sto_xyz:3    0.080420 -0.292910 1.976799 -43.901993
sto_xyz:4    0.000000 0.000000 0.000000 1.000000
sform_xorient    Right-to-Left
sform_yorient    Anterior-to-Posterior
sform_zorient    Inferior-to-Superior
file_type    NIFTI-1+
file_code    1
descrip        6.0.1
aux_file

We noticed that running "${FSLDIR}/bin/fslmaths ${WD}/BothPhases -abs -add 1 
-mas ${WD}/Mask -dilM -dilM -dilM -dilM -dilM ${WD}/BothPhases_fsl5" seems to 
work with FSL 5.0.6 at least. The header of the image "BothPhases_fsl5 ", 
generated with FSL 5.0.6 , is:

filename       BothPhases_fsl5.nii.gz

sizeof_hdr     348
data_type      FLOAT32
dim0           4
dim1           104
dim2           104
dim3           72
dim4           6
dim5           1
dim6           1
dim7           1
vox_units      mm
time_units     s
datatype       16
nbyper         4
bitpix         32
pixdim0        0.000000
pixdim1        2.000000
pixdim2        2.000000
pixdim3        2.000000
pixdim4        7.700000
pixdim5        0.000000
pixdim6        0.000000
pixdim7        0.000000
vox_offset     352
cal_max        0.0000
cal_min        0.0000
scl_slope      1.000000
scl_inter      0.000000
phase_dim      0
freq_dim       0
slice_dim      0
slice_name     Unknown
slice_code     0
slice_start    0
slice_end      0
slice_duration 0.000000
time_offset    0.000000
intent         Unknown
intent_code    0
intent_name
intent_p1      0.000000
intent_p2      0.000000
intent_p3      0.000000
qform_name     Scanner Anat
qform_code     1
qto_xyz:1      -1.995593  0.092717  0.094922  93.702583
qto_xyz:2      -0.105543  -1.976261  -0.288537  118.937881
qto_xyz:3      0.080419  -0.292910  1.976799  -43.901993
qto_xyz:4      0.000000  0.000000  0.000000  1.000000
qform_xorient  Right-to-Left
qform_yorient  Anterior-to-Posterior
qform_zorient  Inferior-to-Superior
sform_name     Scanner Anat
sform_code     1
sto_xyz:1      -1.995594  0.092714  0.094922  93.702583
sto_xyz:2      -0.105540  -1.976261  -0.288537  118.937881
sto_xyz:3      0.080420  -0.292910  1.976799  -43.901993
sto_xyz:4      0.000000  0.000000  0.000000  1.000000
sform_xorient  Right-to-Left
sform_yorient  Anterior-to-Posterior
sform_zorient  Inferior-to-Superior
file_type      NIFTI-1+
file_code      1
descrip        FSL5.0
aux_file


All the best

Simon


>>> Timothy Coalson <tsc...@mst.edu> 05/21/19 8:57 PM >>>
This may not be related to your particular problem, but you need to have FSL 
6.0.1 for some of the pipelines (MR FIX in particular).  Using fslhd on the 
BothPhases and Mask files should give others on the list some information to 
work with.

Tim


On Tue, May 21, 2019 at 8:18 AM Simon Wein 
<simon.w...@psychologie.uni-regensburg.de<mailto:simon.w...@psychologie.uni-regensburg.de>>
 wrote:
Dear all,

we are experiencing problems when performing the fMRI volumetric processing 
with "GenericfMRIVolumeProcessingPipeline.sh":

Image Exception : #3 :: Attempted to multiply images of different sizes
terminate called after throwing an instance of 'std::runtime_error'
  what():  Attempted to multiply images of different sizes
/loctmp/CUDA/Pipelines-master_fs6/global/scripts/TopupPreprocessingAll.sh: line 
269: 10710 Aborted                 ${FSLDIR}/bin/fslmaths ${WD}/BothPhases -abs 
-add 1 -mas ${WD}/Mask -dilM -dilM -dilM -dilM -dilM ${WD}/BothPhases


Environment:
1. Debian 9.0
2. HCP pipeline 4.0.0
3. Workbench 1.3.2
4. FreeSurfer 6.0
5. FSL 6.0
6. gradunwarp (HCP) 1.0.3


We would be thankful for any help!

Kind regards
Simon
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