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 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> 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 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> 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
