Post-Eddy Error (perhaps edd_quad)

[Lin Cai]

Dear HCP-experts,

I am using HCP diffusion pipeline (v4.3) to process my own data for testing whether a new GPU (Gefore RTX 4090) are usable. (FSL 6.0.6 and cuda10.2 are used)

It seems that the Eddy processing was succeed, but there are error messages for post-eddy. 

Could you please help me to fix this issue?

Thank you very much

Lin

From the logfile named DiffPreprocPipeline.sh.e24417, you could find the following error messages for the current subject data.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

...................Allocated GPU # 0...................
Fri Mar  3 15:13:36 JST 2023:run_eddy.sh: Completed with return value: 0
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline_Eddy.sh: Completed!
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline.sh: Invoking Post-Eddy Steps
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline.sh: post_eddy_cmd: /usr/local/HCPpipelines/DiffusionPreprocessing/DiffPreprocPipeline_PostEddy.sh  --path=/mnt/data2/DiffusionTest/derivatives/HCPpipeline  --subject=sub-K2009231730  --dwiname=Diffusion  --gdcoeffs=/mnt/data2/DiffusionTest/code/SimensPrismaKomaba_coeff.grad  --dof=6  --combine-data-flag=1  --printcom=
========================================
  DIRECTORY: /usr/local/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: v4.3.0
========================================
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline_PostEddy.sh: HCPPIPEDIR: /usr/local/HCPpipelines
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline_PostEddy.sh: FSLDIR: /usr/local/fsl
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline_PostEddy.sh: HCPPIPEDIR_Global: /usr/local/HCPpipelines/global/scripts
-- DiffPreprocPipeline_PostEddy.sh: Specified Command-Line Parameters - Start --
   StudyFolder: /mnt/data2/DiffusionTest/derivatives/HCPpipeline
   Subject: sub-K2009231730
   DWIName: Diffusion
   GdCoeffs: /mnt/data2/DiffusionTest/code/SimensPrismaKomaba_coeff.grad
   DegreesOfFreedom: 6
   runcmd:
   CombineDataFlag: 1
   SelectBestB0: false
-- DiffPreprocPipeline_PostEddy.sh: Specified Command-Line Parameters - End --
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline_PostEddy.sh: Gradient nonlinearity distortion correction coefficients found!
Fri Mar  3 15:13:36 JST 2023:DiffPreprocPipeline_PostEddy.sh: Running Eddy PostProcessing

 START: eddy_postproc
Generating eddy QC report in /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC
found b-shell of 14 orientations with b-value 5.000000
found b-shell of 92 orientations with b-value 1495.000000
found b-shell of 92 orientations with b-value 2995.000000
found b-shell of 6 orientations with b-value 200.000000
found b-shell of 12 orientations with b-value 497.000000
Fri Mar  3 15:13:38 JST 2023:eddy_postproc.sh: ERROR: '/usr/local/fsl/bin/eddy_quad' command failed with return code: 1

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: eddy_postproc.sh
stopped at line: 35
           call: "${qc_command[@]}"
  expanded call: /usr/local/fsl/bin/eddy_quad /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/eddy_unwarped_images -idx /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/index.txt -par /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/acqparams.txt -m /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/nodif_brain_mask.nii.gz -b /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/Pos_Neg.bvals -g /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/eddy_unwarped_images.eddy_rotated_bvecs -o /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC -f /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/topup/topup_Pos_Neg_b0_field.nii.gz -v
      exit code: 1
---------------------------------------------------

===> Aborting execution!

Fri Mar  3 15:13:38 JST 2023:DiffPreprocPipeline_PostEddy.sh: Running Diffusion to Structural Registration

 START: DiffusionToStructural
Running FAST segmentation
FLIRT pre-alignment
Running BBR
Fri Mar  3 15:21:49 JST 2023:DiffusionToStructural.sh: ERROR: '/usr/local/fsl/bin/applywarp' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: DiffusionToStructural.sh
stopped at line: 59
           call: ${FSLDIR}/bin/applywarp --rel --interp=spline -i "$DataDirectory"/"$regimg" -r "$T1wImage" --premat="$WorkingDirectory"/"$regimg"2T1w_initII_init.mat -o "$WorkingDirectory"/"$regimg"2T1w_init.nii.gz
  expanded call: /usr/local/fsl/bin/applywarp --rel --interp=spline -i /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif -r /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc --premat=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_initII_init.mat -o /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_init.nii.gz
      exit code: 134
---------------------------------------------------

===> Aborting execution!

Fri Mar  3 15:21:49 JST 2023:DiffPreprocPipeline_PostEddy.sh: Copying eddy log files to package location: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/Diffusion/eddylogs
Could not find a supported file with prefix "/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/Diffusion/cnr_maps"
Fri Mar  3 15:21:49 JST 2023:DiffPreprocPipeline_PostEddy.sh: Completed!
Fri Mar  3 15:21:49 JST 2023:DiffPreprocPipeline.sh: Completed!

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

From the DiffPreprocPipeline.sh.e24417, you could see the following messages.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Traceback (most recent call last):
  File "/usr/local/fsl/bin/eddy_quad", line 52, in <module>
    main(args.eddyBase, args.eddyIdx, args.eddyParams, args.mask, args.bvals, args.bvecs, args.output_dir, args.field, args.slspec, args.json, args.verbose)
  File "/usr/local/fsl/lib/python3.10/site-packages/eddy_qc/QUAD/quad.py", line 208, in main
    'mask':mask_vol.get_data(),
  File "/usr/local/fsl/lib/python3.10/site-packages/nibabel/deprecator.py", line 185, in deprecated_func
    raise error_class(message)
nibabel.deprecator.ExpiredDeprecationError: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Raises <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
Fri Mar  3 15:13:38 JST 2023:eddy_postproc.sh: While running '/usr/local/HCPpipelines/DiffusionPreprocessing/scripts/eddy_postproc.sh /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion /mnt/data2/DiffusionTest/code/SimensPrismaKomaba_coeff.grad 1 0':
Fri Mar  3 15:13:38 JST 2023:eddy_postproc.sh: ERROR: '/usr/local/fsl/bin/eddy_quad' command failed with return code: 1
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/data
No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/data
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Could not open matrix file /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_initII.mat
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
terminate called after throwing an instance of 'std::runtime_error'
  what():  Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
/usr/local/HCPpipelines/global/scripts/epi_reg_dof: line 386: 13696 Aborted                 (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
Could not open matrix file /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_initII_init.mat
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
terminate called after throwing an instance of 'std::runtime_error'
  what():  Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
/usr/local/HCPpipelines/DiffusionPreprocessing/scripts/DiffusionToStructural.sh: line 59: 13726 Aborted                 (core dumped) ${FSLDIR}/bin/applywarp --rel --interp=spline -i "$DataDirectory"/"$regimg" -r "$T1wImage" --premat="$WorkingDirectory"/"$regimg"2T1w_initII_init.mat -o "$WorkingDirectory"/"$regimg"2T1w_init.nii.gz
Fri Mar  3 15:21:49 JST 2023:DiffusionToStructural.sh: While running '/usr/local/HCPpipelines/DiffusionPreprocessing/scripts/DiffusionToStructural.sh --t1folder=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w --subject=sub-K2009231730 --workingdir=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg --datadiffdir=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data --t1=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc --t1restore=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc_restore --t1restorebrain=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc_restore_brain --biasfield=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/BiasField_acpc_dc --brainmask=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/brainmask_fs --datadiffT1wdir=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/Diffusion --regoutput=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/Scout2T1w --QAimage=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/T1wMulEPI --dof=6 --gdflag=1 --diffresol=0.00':
Fri Mar  3 15:21:49 JST 2023:DiffusionToStructural.sh: ERROR: '/usr/local/fsl/bin/applywarp' command failed with return code: 134
cp: cannot stat '/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/*': No such file or directory

[Glasser, Matt]

This looks like it might be an FSL bug.  Could you send them the first .e portion about the eddy_quad deprecation stuff (i.e., before the image exception stuff? 

 

Matt.

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[Lin Cai]

Hi Matt,

I have updated FSL version and eddy qc packages according to Paul's response.

(https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2303&L=FSL&O=D&X=7D0981C6902879578D&Y=bertram0611%40gmail.com&P=94883)

From the new error messages as follows, it seems there is something wrong with the /usr/local/HCPpipelines/global/scripts/average_bvecs.py

Could you please help me check these two log files again.

Thank you very much.

Lin

##########################################-----------DiffPreprocPipeline.sh.o5333---------#################################################

Tue Mar 14 10:23:49 JST 2023:DiffPreprocPipeline_PostEddy.sh: HCPPIPEDIR: /usr/local/HCPpipelines

Tue Mar 14 10:23:49 JST 2023:DiffPreprocPipeline_PostEddy.sh: FSLDIR: /usr/local/fsl
Tue Mar 14 10:23:49 JST 2023:DiffPreprocPipeline_PostEddy.sh: HCPPIPEDIR_Global: /usr/local/HCPpipelines/global/scripts

-- DiffPreprocPipeline_PostEddy.sh: Specified Command-Line Parameters - Start --
   StudyFolder: /mnt/data2/DiffusionTest/derivatives/HCPpipeline
   Subject: sub-K2009231730
   DWIName: Diffusion
   GdCoeffs: /mnt/data2/DiffusionTest/code/SimensPrismaKomaba_coeff.grad
   DegreesOfFreedom: 6
   runcmd:
   CombineDataFlag: 1
   SelectBestB0: false
-- DiffPreprocPipeline_PostEddy.sh: Specified Command-Line Parameters - End --

Tue Mar 14 10:23:49 JST 2023:DiffPreprocPipeline_PostEddy.sh: Gradient nonlinearity distortion correction coefficients found!
Tue Mar 14 10:23:49 JST 2023:DiffPreprocPipeline_PostEddy.sh: Running Eddy PostProcessing

 START: eddy_postproc
Generating eddy QC report in /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC
found b-shell of 14 orientations with b-value 5.000000
found b-shell of 92 orientations with b-value 1495.000000
found b-shell of 92 orientations with b-value 2995.000000
found b-shell of 6 orientations with b-value 200.000000
found b-shell of 12 orientations with b-value 497.000000

RMS movement estimates file detected
Eddy parameters file detected
Outliers output files detected
CNR output files detected
Topup fieldmap file detected
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b0_pe0 -i 0 7990.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b0_pe0.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b0_pe1 -i 0 8081.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b0_pe1.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/vdm -i -7.0 7.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/vdm.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b0 -i 0 7924.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b0.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b200 -i 0 5471.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b200.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b497 -i 0 4226.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b497.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b1495 -i 0 2336.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b1495.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b2995 -i 0 1256.0 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/avg_b2995.png
Running $FSLDIR/bin/fslsplit /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/eddy_unwarped_images.eddy_cnr_maps.nii.gz /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0000.nii.gz -i 0 39.42 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0000.nii.gz.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0001.nii.gz -i 0 1.94 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0001.nii.gz.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0002.nii.gz -i 0 2.34 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0002.nii.gz.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0003.nii.gz -i 0 2.33 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0003.nii.gz.png
Running $FSLDIR/bin/slicer /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0004.nii.gz -i 0 2.48 -a /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/QC/cnr0004.nii.gz.png
JAC resampling has been used. Eddy Output is now combined.
Number of sessions per data set:      1
Number of volumes in first data set:  108
Number of volumes in second data set: 108
Session 1 overlaps:          108.0
Data set 1 session 1 offset: 0
Data set 2 session 1 offset: 0
Tue Mar 14 10:27:11 JST 2023:eddy_postproc.sh: ERROR: '/usr/local/HCPpipelines/global/scripts/average_bvecs.py' command failed with return code: 1

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: eddy_postproc.sh

stopped at line: 117
           call: ${globalscriptsdir}/average_bvecs.py ${eddydir}/Pos.bval ${eddydir}/Pos_rotated.bvec ${eddydir}/Neg.bval ${eddydir}/Neg_rotated.bvec ${datadir}/avg_data ${CombineDataFlag} ${eddydir}/Pos_SeriesVolNum.txt ${eddydir}/Neg_SeriesVolNum.txt
  expanded call: /usr/local/HCPpipelines/global/scripts/average_bvecs.py /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/Pos.bval /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/Pos_rotated.bvec /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/Neg.bval /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/Neg_rotated.bvec /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/avg_data 1 /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/Pos_SeriesVolNum.txt /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/eddy/Neg_SeriesVolNum.txt

      exit code: 1
---------------------------------------------------

===> Aborting execution!

Tue Mar 14 10:27:11 JST 2023:DiffPreprocPipeline_PostEddy.sh: Running Diffusion to Structural Registration

 START: DiffusionToStructural
Running FAST segmentation
FLIRT pre-alignment
Running BBR

Tue Mar 14 10:35:00 JST 2023:DiffusionToStructural.sh: ERROR: '/usr/local/fsl/bin/applywarp' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: DiffusionToStructural.sh
stopped at line: 59
           call: ${FSLDIR}/bin/applywarp --rel --interp=spline -i "$DataDirectory"/"$regimg" -r "$T1wImage" --premat="$WorkingDirectory"/"$regimg"2T1w_initII_init.mat -o "$WorkingDirectory"/"$regimg"2T1w_init.nii.gz
  expanded call: /usr/local/fsl/bin/applywarp --rel --interp=spline -i /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif -r /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc --premat=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_initII_init.mat -o /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_init.nii.gz
      exit code: 134
---------------------------------------------------

===> Aborting execution!

Tue Mar 14 10:35:00 JST 2023:DiffPreprocPipeline_PostEddy.sh: Copying eddy log files to package location: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/Diffusion/eddylogs

Could not find a supported file with prefix "/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/Diffusion/cnr_maps"

Tue Mar 14 10:35:00 JST 2023:DiffPreprocPipeline_PostEddy.sh: Completed!
Tue Mar 14 10:35:00 JST 2023:DiffPreprocPipeline.sh: Completed!

##########################################-----------DiffPreprocPipeline.sh.e5333---------#################################################

Traceback (most recent call last):

  File "/usr/local/HCPpipelines/global/scripts/average_bvecs.py", line 320, in <module>
    main(bvals1,      bvecs1,
  File "/usr/local/HCPpipelines/global/scripts/average_bvecs.py", line 79, in main
    bvals1, bvecs1, bvals2, bvecs2, indices1, indices2 = extract_overlaps(
  File "/usr/local/HCPpipelines/global/scripts/average_bvecs.py", line 180, in extract_overlaps
    bv1_indices = np.arange(offset1, offset1 + overlaps, dtype=np.int)
  File "/home/klab/.local/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'inf'?
Tue Mar 14 10:27:11 JST 2023:eddy_postproc.sh: While running '/usr/local/HCPpipelines/DiffusionPreprocessing/scripts/eddy_postproc.sh /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion /mnt/data2/DiffusionTest/code/SimensPrismaKomaba_coeff.grad 1 0':
Tue Mar 14 10:27:11 JST 2023:eddy_postproc.sh: ERROR: '/usr/local/HCPpipelines/global/scripts/average_bvecs.py' command failed with return code: 1

Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Could not open matrix file /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_initII.mat
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
terminate called after throwing an instance of 'std::runtime_error'
  what():  Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif

/usr/local/HCPpipelines/global/scripts/epi_reg_dof: line 386: 33971 Aborted                 (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline

Could not open matrix file /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/nodif2T1w_initII_init.mat
Image Exception : #63 :: No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Image Exception : #22 :: Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
terminate called after throwing an instance of 'std::runtime_error'
  what():  Failed to read volume /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif
Error : No image files match: /mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif

/usr/local/HCPpipelines/DiffusionPreprocessing/scripts/DiffusionToStructural.sh: line 59: 33979 Aborted                 (core dumped) ${FSLDIR}/bin/applywarp --rel --interp=spline -i "$DataDirectory"/"$regimg" -r "$T1wImage" --premat="$WorkingDirectory"/"$regimg"2T1w_initII_init.mat -o "$WorkingDirectory"/"$regimg"2T1w_init.nii.gz
Tue Mar 14 10:35:00 JST 2023:DiffusionToStructural.sh: While running '/usr/local/HCPpipelines/DiffusionPreprocessing/scripts/DiffusionToStructural.sh --t1folder=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w --subject=sub-K2009231730 --workingdir=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg --datadiffdir=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data --t1=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc --t1restore=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc_restore --t1restorebrain=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/T1w_acpc_dc_restore_brain --biasfield=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/BiasField_acpc_dc --brainmask=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/brainmask_fs --datadiffT1wdir=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/T1w/Diffusion --regoutput=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/Scout2T1w --QAimage=/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/reg/T1wMulEPI --dof=6 --gdflag=1 --diffresol=1.50':
Tue Mar 14 10:35:00 JST 2023:DiffusionToStructural.sh: ERROR: '/usr/local/fsl/bin/applywarp' command failed with return code: 134

2023年3月3日金曜日 22:38:52 UTC+9 glas...@wustl.edu:

[Glasser, Matt]

Does this file get created:

 

/mnt/data2/DiffusionTest/derivatives/HCPpipeline/sub-K2009231730/Diffusion/data/nodif

 

CCing Michel Cottaar in case he can help.

[Lin Cai]

Hi Matt,

There are no such files named nodif (e.g., nodif.nii.gz, nodif_brain_mask.nii.gz, nodif_brain.nii.gz).

Thank you very much for CCing Michel Cottaar.

Best,

Lin

--

Lin Cai

Project Researcher

University of Tokyo, Center for Evolutionary Cognitive Sciences

Tokyo, Japan

[Glasser, Matt]

Looking at this again, I think the issue is in the python code HCPpipelines/global/scripts/average_bvecs.py using a deprecated function.  Perhaps this is an easy fix for Tim or Alex?

[Yang, Chunhui]

Hi Lin,

The issue is caused by the deprecation of “np.int” after Numpy 1.20.0. A quick fix is to replace any “np.int” with just python “int” in the script HCPpipelines/global/scripts/average_bvecs.py.

For example, in line 180, change it from

bv1_indices = np.arange(offset1, offset1 + overlaps, dtype=np.int)

To 

bv1_indices = np.arange(offset1, offset1 + overlaps, dtype=int)

Please let me know if this fix works then I will create a PR to fix it in the official pipeline.

Thanks,

Alex

---

From: Glasser, Matt <glas...@wustl.edu>
Sent: Wednesday, March 15, 2023 6:13 AM
To: Lin Cai <bertr...@gmail.com>
Cc: HCP-Users <hcp-...@humanconnectome.org>; Michiel Cottaar <michiel...@ndcn.ox.ac.uk>; Coalson, Timothy <coal...@wustl.edu>; Yang, Chunhui <chunh...@wustl.edu>

[Lin Cai]

Hi Alex and Matt,

Thank you very much for debugging.

The bugs were fixed after I replaced all "np.int" with "int" in the script HCPpipelines/global/scripts/average_bvecs.py.

The raw diffusion data has been preprocessed successfully this time, while there is only a small warning as follows.

I think it is fine, isn't it?

Lin

 

################------------DiffPreprocPipeline.sh.e20698----------##################### 
gradunwarp-INFO: Parsing /mnt/data2/DiffusionTest/code/SimensPrismaKomaba_coeff.grad for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
gradunwarp-INFO: Writing output to trilinear.nii.gz
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.