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 <[email protected]> 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
<[email protected]> 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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