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
${WD}/SBRef2PhaseTwo_gdc
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX
On Sat, May 25, 2019 at 8:48 AM Simon Wein <
simon.w...@psychologie.uni-regensburg.de> wrote:
> Thank you very much for your support.
> In our pipeline we have set *$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:
>
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> *filename Mask.nii.gzsize of header 348data_type FLOAT32dim0
> 4dim1 104dim2 104dim3 72dim4 6dim5
> 1dim6 1dim7 1vox_units mmtime_units sdatatype
> 16nbyper 4bitpix 32pixdim0 1.000000pixdim1
> 2.000000pixdim2 2.000000pixdim3 2.000000pixdim4
> 7.700000pixdim5 0.000000pixdim6 0.000000pixdim7
> 0.000000vox_offset 352cal_max 0.000000cal_min
> 0.000000scl_slope 1.000000scl_inter 0.000000phase_dim 0freq_dim
> 0slice_dim 0slice_name Unknownslice_code 0slice_start
> 0slice_end 0slice_duration 0.000000toffset 0.000000intent
> Unknownintent_code 0intent_name intent_p1 0.000000intent_p2
> 0.000000intent_p3 0.000000qform_name Scanner Anatqform_code
> 1qto_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-Leftqform_yorient
> Anterior-to-Posteriorqform_zorient Inferior-to-Superiorsform_name
> Scanner Anatsform_code 1sto_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-Leftsform_yorient
> Anterior-to-Posteriorsform_zorient Inferior-to-Superiorfile_type
> NIFTI-1+file_code 1descrip 6.0.1aux_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.matCannot
> 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:
>
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> *filename SBRef.nii.gzsize of header 348data_type UINT16dim0
> 3dim1 104dim2 104dim3 72dim4 1dim5
> 0dim6 0dim7 0vox_units mmtime_units sdatatype
> 512nbyper 2bitpix 16pixdim0 1.000000pixdim1
> 2.000000pixdim2 2.000000pixdim3 2.000000pixdim4
> 0.730000pixdim5 0.000000pixdim6 0.000000pixdim7
> 0.000000vox_offset 352cal_max 0.000000cal_min
> 0.000000scl_slope 1.000000scl_inter 0.000000phase_dim 2freq_dim
> 1slice_dim 3slice_name sequential_increasingslice_code
> 1slice_start 0slice_end 0slice_duration 0.000000toffset
> 0.000000intent Unknownintent_code 0intent_name intent_p1
> 0.000000intent_p2 0.000000intent_p3 0.000000qform_name Scanner
> Anatqform_code 1qto_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-Leftqform_yorient
> Anterior-to-Posteriorqform_zorient Inferior-to-Superiorsform_name
> Scanner Anatsform_code 1sto_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-Leftsform_yorient
> Anterior-to-Posteriorsform_zorient Inferior-to-Superiorfile_type
> NIFTI-1+file_code 1descrip
> TE=31;Time=163300.630;phase=0aux_file Single-band_reference*
>
>
> And properties of *PhaseTwo_gdc.nii.gz:*
>
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>
> *filename PhaseTwo_gdc.nii.gzsize of header 348data_type
> UINT16dim0 4dim1 104dim2 104dim3 72dim4
> 3dim5 0dim6 0dim7 0vox_units mmtime_units
> sdatatype 512nbyper 2bitpix 16pixdim0
> 1.000000pixdim1 2.000000pixdim2 2.000000pixdim3
> 2.000000pixdim4 7.700000pixdim5 0.000000pixdim6
> 0.000000pixdim7 0.000000vox_offset 352cal_max
> 0.000000cal_min 0.000000scl_slope 1.000000scl_inter
> 0.000000phase_dim 2freq_dim 1slice_dim 3slice_name
> alternating_increasing_2slice_code 5slice_start 0slice_end
> 0slice_duration 0.000000toffset 0.000000intent
> Unknownintent_code 0intent_name intent_p1 0.000000intent_p2
> 0.000000intent_p3 0.000000qform_name Scanner Anatqform_code
> 1qto_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-Leftqform_yorient
> Anterior-to-Posteriorqform_zorient Inferior-to-Superiorsform_name
> Scanner Anatsform_code 1sto_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-Leftsform_yorient
> Anterior-to-Posteriorsform_zorient Inferior-to-Superiorfile_type
> NIFTI-1+file_code 1descrip
> TE=58;Time=162508.120;phase=0aux_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
> <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> 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:
>
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> *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 ${WD}/Mask.nii.gz" is:
>
>
>
> *filename Mask.nii.gz*
>
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> * size of header 348 data_type FLOAT32 dim0 4 dim1 104
> dim2 104 dim3 72 dim4 3 dim5 1 dim6 1
> dim7 1 vox_units mm time_units s datatype 16 nbyper
> 4 bitpix 32 pixdim0 1.000000 pixdim1 2.000000
> pixdim2 2.000000 pixdim3 2.000000 pixdim4 7.700000
> pixdim5 0.000000 pixdim6 0.000000 pixdim7 0.000000
> vox_offset 352 cal_max 0.000000 cal_min 0.000000
> scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0
> slice_dim 0 slice_name Unknown slice_code 0 slice_start 0
> slice_end 0 slice_duration 0.000000 toffset 0.000000 intent
> Unknown intent_code 0 intent_name intent_p1 0.000000
> intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat
> qform_code 1 qto_xyz:1 -1.995593 0.092717 0.094922 93.702583
> qto_xyz:2 -0.105543 -1.976261 -0.288537 118.937881 qto_xyz:3 0.080419
> -0.292910 1.976799 -43.901993 qto_xyz:4 0.000000 0.000000 0.000000
> 1.000000 qform_xorient Right-to-Left qform_yorient
> Anterior-to-Posterior qform_zorient Inferior-to-Superior sform_name
> Scanner Anat sform_code 1 sto_xyz:1 -1.995594 0.092714 0.094922
> 93.702583 sto_xyz:2 -0.105540 -1.976261 -0.288537 118.937881
> sto_xyz:3 0.080420 -0.292910 1.976799 -43.901993 sto_xyz:4 0.000000
> 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient
> Anterior-to-Posterior sform_zorient Inferior-to-Superior file_type
> NIFTI-1+ file_code 1 descrip 6.0.1 aux_file *
>
>
>
> We noticed that running "*${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:
>
>
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>
> *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
>
> _______________________________________________
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>
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>
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