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MASILab / Synb0-DISCO

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps
https://my.vanderbilt.edu/masi
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pipeline.sh: missing files? #55

Open ckindler123 opened 9 months ago

ckindler123 commented 9 months ago

Hi there,

We tried to get Synb0-DISCO run using docker and got an error message (see at the bottom of the email). The script pipeline.sh uses the files /extra/dual_channel_unet/numfold"$i"total_folds"$NUM_FOLDS"seed_1_num_epochs_100_lr_0.0001_betas(0.9,\ 0.999)weight_decay_1e-05_num_epoch*.pth We do not know, what is the path to the files in docker, but in the folders in Github we found the files in the folder src/train_lin. Could that be the reason for pipeline.sh not to find the files and how to fix it?

Thank you for your help!

Copying results to results path...

Removing job directory... Performing inference on FOLD: 1 /extra/pipeline.sh: line 42: 1194 Killed python3.6 /extra/inference.py /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz /OUTPUTS/b0_u_lin_atlas_2_5FOLD"$i".nii.gz /extra/dual_channel_unet/numfold"$i"_totalfolds"$NUM_FOLDS"_seed_1_num_epochs_100_lr_0.0001betas(0.9\,\ 0.999)_weight_decay_1e-05_numepoch.pth Performing inference on FOLD: 2 /extra/pipeline.sh: line 42: 1394 Killed python3.6 /extra/inference.py /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz /OUTPUTS/b0_u_lin_atlas_2_5FOLD"$i".nii.gz /extra/dual_channel_unet/numfold"$i"_totalfolds"$NUM_FOLDS"_seed_1_num_epochs_100_lr_0.0001betas(0.9\,\ 0.999)_weight_decay_1e-05_numepoch.pth Performing inference on FOLD: 3 /extra/pipeline.sh: line 42: 1594 Killed python3.6 /extra/inference.py /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz /OUTPUTS/b0_u_lin_atlas_2_5FOLD"$i".nii.gz /extra/dual_channel_unet/numfold"$i"_totalfolds"$NUM_FOLDS"_seed_1_num_epochs_100_lr_0.0001betas(0.9\,\ 0.999)_weight_decay_1e-05_numepoch.pth Performing inference on FOLD: 4 Performing inference on FOLD: 5 /extra/pipeline.sh: line 42: 1794 Killed python3.6 /extra/inference.py /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz /OUTPUTS/b0_u_lin_atlas_2_5FOLD"$i".nii.gz /extra/dual_channel_unet/numfold"$i"_totalfolds"$NUM_FOLDS"_seed_1_num_epochs_100_lr_0.0001betas(0.9\,\ 0.999)_weight_decay_1e-05_numepoch.pth /extra/pipeline.sh: line 42: 1994 Killed python3.6 /extra/inference.py /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz /OUTPUTS/b0_u_lin_atlas_2_5FOLD"$i".nii.gz /extra/dual_channel_unet/numfold"$i"_totalfolds"$NUM_FOLDS"_seed_1_num_epochs_100_lr_0.0001betas(0.9\,\ 0.999)_weight_decay_1e-05_numepoch.pth Taking ensemble average Image Exception : #63 :: No image files match: /OUTPUTS/b0_u_lin_atlas_2_5FOLD terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /OUTPUTS/b0_u_lin_atlas_2_5FOLD /extra/pipeline.sh: line 49: 2194 Aborted fslmerge -t /OUTPUTS/b0_u_lin_atlas_2_5_merged.nii.gz /OUTPUTS/b0_u_lin_atlas_2_5FOLD.nii.gz Image Exception : #63 :: No image files match: /OUTPUTS/b0_u_lin_atlas_2_5_merged terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /OUTPUTS/b0_u_lin_atlas_2_5_merged /extra/pipeline.sh: line 50: 2195 Aborted fslmaths /OUTPUTS/b0_u_lin_atlas_2_5_merged.nii.gz -Tmean /OUTPUTS/b0_u_lin_atlas_2_5.nii.gz Applying inverse xform to undistorted b0 file /OUTPUTS/b0_u_lin_atlas_2_5.nii.gz does not exist . terminate called after throwing an instance of 'itk::ExceptionObject' what(): /home/local/VANDERBILT/blaberj/ANTS_13_FEB_2019/bin/ants/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1412: itk::ERROR: ResampleImageFilter(0x2e5c700): Input Primary is required but not set. /extra/pipeline.sh: line 54: 2196 Aborted antsApplyTransforms -d 3 -i /OUTPUTS/b0_u_lin_atlas_2_5.nii.gz -r /INPUTS/b0.nii.gz -n BSpline -t [/OUTPUTS/epi_reg_d_ANTS.txt,1] -t [/OUTPUTS/ANTS0GenericAffine.mat,1] -o /OUTPUTS/b0_u.nii.gz Applying slight smoothing to distorted b0 Running topup Image Exception : #63 :: No image files match: /OUTPUTS/b0_u terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /OUTPUTS/b0_u /extra/pipeline.sh: line 65: 2207 Aborted fslmerge -t /OUTPUTS/b0_all.nii.gz /OUTPUTS/b0_d_smooth.nii.gz /OUTPUTS/b0_u.nii.gz Image Exception : #63 :: No image files match: /OUTPUTS/b0_all Image Exception : #22 :: Failed to read volume /OUTPUTS/b0_all.nii.gz Error : No image files match: /OUTPUTS/b0_all

Part of FSL (ID: 6.0.1) topup

Usage: topup --imain=<some 4D image> --datain= --config= --out=my_topup_results

Compulsory arguments (You MUST set one or more of): --imain name of 4D file with images --datain name of text file with PE directions/times

Optional arguments (You may optionally specify one or more of): --out base-name of output files (spline coefficients (Hz) and movement parameters) --fout name of image file with field (Hz) --iout name of 4D image file with unwarped images --logout Name of log-file --warpres (approximate) resolution (in mm) of warp basis for the different sub-sampling levels, default 10 --subsamp sub-sampling scheme, default 1 --fwhm FWHM (in mm) of gaussian smoothing kernel, default 8 --config Name of config file specifying command line arguments --miter Max # of non-linear iterations, default 5 --lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation. --ssqlambda If set (=1), lambda is weighted by current ssq, default 1 --regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy --estmov Estimate movements if set, default 1 (true) --minmet Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM) --splineorder Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3 --numprec Precision for representing Hessian, double or float. Default double --interp Image interpolation model, linear or spline. Default spline --scale If set (=1), the images are individually scaled to a common mean, default 0 (false) --regrid If set (=1), the calculations are done in a different grid, default 1 (true) -h,--help display help info -v,--verbose Print diagonostic information while running -h,--help display help info

Failed to read volume /OUTPUTS/b0_all.nii.gz Error : No image files match: /OUTPUTS/b0_all FINISHED!!!

MattRicchi commented 8 months ago

Hello, I'm having the same issue. Did you manage to solve it by any chance?

Thank youfor your help!

ckindler123 commented 8 months ago

Hi Mattia,

 

yes, we could solve the problem! It was the RAM - the command needs more than 16 RAM and abort when the 16 RAM are reached. Now it works on a another laptop with 32 RAM. Hope it helps!

 

Best wishes

Christine

   

Gesendet: Donnerstag, 09. November 2023 um 16:01 Uhr Von: "Mattia Ricchi" @.> An: "MASILab/Synb0-DISCO" @.> Cc: "ckindler123" @.>, "Author" @.> Betreff: Re: [MASILab/Synb0-DISCO] pipeline.sh: missing files? (Issue #55)

 

Hello, I'm having the same issue. Did you manage to solve it by any chance?

Thank youfor your help!

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