Try the very latest master, which should resolve this issue. (I was just
working on this 30 min ago). Please let us know if it works.
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: <hcp-users-boun...@humanconnectome.org> on behalf of Joseph Orr
<joseph....@tamu.edu>
Date: Wednesday, June 5, 2019 at 1:52 PM
To: Simon Wein <simon.w...@psychologie.uni-regensburg.de>
Cc: HCP Users <hcp-users@humanconnectome.org>, Wilhelm Malloni
<wilhelm.mall...@psychologie.uni-regensburg.de>
Subject: Re: [HCP-Users] Error while running
"GenericfMRIVolumeProcessingPipeline.sh"
We ran into the same problem with flirt. In FSL 6.0.1, flirt can't take a 4D
file as a reference, but it could in fsl v5. Adding a line before 289 to
extract the first volume of PhaseTwo_gdc, and modifying flirt accordingly fixes
the problem:
${FSLDIR}/bin/fslroi ${WD}/PhaseTwo_gdc ${WD}/PhaseTwo_gdc_slice -1 -1 -1 -1 -1
-1 0 1
${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref
${WD}/PhaseTwo_gdc_slice -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out
${WD}/SBRef2PhaseTwo_gdc
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX
On Sat, May 25, 2019 at 8:48 AM Simon Wein
<simon.w...@psychologie.uni-regensburg.de<mailto:simon.w...@psychologie.uni-regensburg.de>>
wrote:
Thank you very much for your support.
In our pipeline we have set $GradientDistortionCoeffs = "NONE", so line 189 in
https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_HCPpipelines_blob_master_global_scripts_TopupPreprocessingAll.sh&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=THI4wxtmV_mHRAFlqo6fSROIYYps7PUMkLs13L56dHs&s=8WyIfhjNJpj6y0N1VFd0l72m8q5_3JN4yAteiQWVgIM&e=>
was unfortunately skipped. But we could avoid the error by modifying line 196
to:
fslmaths ${WD}/BothPhases.nii.gz -mul 0 -add 1 ${WD}/Mask
Mask.nii.gz then has properties:
filename Mask.nii.gz
size of header 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 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 previously mentioned problem with FSL 6.0+ fslmaths could be avoided.
Would you consider this as a good workaround, or would you recommend something
else?
But in a later stage, we got another error:
Image Exception : #75 :: 3D only method called by higher-dimensional volume.
3D only method called by higher-dimensional volume.
Could not open matrix file
/loctmp/CUDA/DATA/VP_101/rfMRI_REST1_PA/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef2PhaseTwo_gdc.mat
Cannot read input-matrix
The file "SBRef2PhaseTwo_gdc.mat" was not created, so the problem might be in
line 289 in "TopupPreprocessingAll.sh":
${FSLDIR}/bin/flirt -dof 6 -interp spline -in ${WD}/SBRef.nii.gz -ref
${WD}/PhaseTwo_gdc -omat ${WD}/SBRef2PhaseTwo_gdc.mat -out
${WD}/SBRef2PhaseTwo_gdc
Properties of SBRef.nii.gz are:
filename SBRef.nii.gz
size of header 348
data_type UINT16
dim0 3
dim1 104
dim2 104
dim3 72
dim4 1
dim5 0
dim6 0
dim7 0
vox_units mm
time_units s
datatype 512
nbyper 2
bitpix 16
pixdim0 1.000000
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 0.730000
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 2
freq_dim 1
slice_dim 3
slice_name sequential_increasing
slice_code 1
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 TE=31;Time=163300.630;phase=0
aux_file Single-band_reference
And properties of PhaseTwo_gdc.nii.gz:
filename PhaseTwo_gdc.nii.gz
size of header 348
data_type UINT16
dim0 4
dim1 104
dim2 104
dim3 72
dim4 3
dim5 0
dim6 0
dim7 0
vox_units mm
time_units s
datatype 512
nbyper 2
bitpix 16
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 2
freq_dim 1
slice_dim 3
slice_name alternating_increasing_2
slice_code 5
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 TE=58;Time=162508.120;phase=0
aux_file
Employing flirt from FSL 5.0.6 worked again, but we were not sure, how to
modify line 289 properly for FSL 6.0.1.
Thank you for your time.
Simon
>>> "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> 05/22/19
>>> 9:09 PM >>>
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<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_HCPpipelines_blob_master_global_scripts_TopupPreprocessingAll.sh&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=THI4wxtmV_mHRAFlqo6fSROIYYps7PUMkLs13L56dHs&s=8WyIfhjNJpj6y0N1VFd0l72m8q5_3JN4yAteiQWVgIM&e=>
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<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Simon Wein
<simon.w...@psychologie.uni-regensburg.de<mailto:simon.w...@psychologie.uni-regensburg.de>>
Date: Wednesday, May 22, 2019 at 8:28 AM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: Wilhelm Malloni
<wilhelm.mall...@psychologie.uni-regensburg.de<mailto:wilhelm.mall...@psychologie.uni-regensburg.de>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto: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<mailto: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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The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
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