Open Meryam1985 opened 2 years ago
hanscol
commented
2 years ago Hello, It looks like you are missing the path to link the freesurfer license within the docker in your command
-v /media/docc/freesurfer-linux-centos6_x86_64-7.1.1/freesurfer/license.txt:/extra/freesurfer/license.txt
Let us know if you still see an error with this.
Meryam1985
commented
2 years ago Thank you very much for your cooperation, I tried with this command: sudo docker run --rm \ -v /media/docc/ses-001use_sb0/anat/:/INPUTS/ \ -v /media/docc/ses-001use_sb0/anat/out:/OUTPUTS/ \ -v /media/docc/freesurfer-linux-centos6_x86_64-7.1.1/freesurfer/license.txt:/extra/freesurfer/license.txt \ --user $(id -u):$(id -g) \ hansencb/synb0 Unfortunately, here is the error message I received: Elapsed time (stage 2): 244.1
Removing job directory... Performing inference on FOLD: 1 T1 input path: /OUTPUTS/T1_norm_lin_atlas_2_5.nii.gz b0 input path: /OUTPUTS/b0_d_lin_atlas_2_5.nii.gz b0 output path: /OUTPUTS/b0_u_lin_atlas_2_5_FOLD_1.nii.gz Model path: /extra/dual_channel_unet/num_fold_1_total_folds_5_seed_1_num_epochs_100_lr_0.0001betas(0.9, 0.999)_weight_decay_1e-05_num_epoch_97.pth Traceback (most recent call last): File "/extra/pytorch/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: '/OUTPUTS/b0_d_lin_atlas_2_5.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/extra/inference.py", line 90, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/extra/inference.py", line 90, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/extra/inference.py", line 90, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/extra/inference.py", line 90, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/extra/inference.py", line 90, in
Part of FSL (ID: 6.0.1) topup
Usage:
topup --imain=<some 4D image> --datain=
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!!!
hanscol
commented
2 years ago It looks like the epi_reg might have failed, but I can’t be sure without the full output log. Could you provide all of the output text in a txt file? That would make things easier. Also could you check if you are providing the full DWI or just the b0 image in the input directory. That may be the issue.
Meryam1985
commented
2 years ago Hello here is attached the totality of the answer and error. also a screenshot of the files used. Cordially.
Le vendredi 3 septembre 2021, 17:12:25 UTC+2, Colin Hansen ***@***.***> a écrit : It looks like the epi_reg might have failed, but I can’t be sure without the full output log. Could you provide all of the output text in a txt file? That would make things easier. Also could you check if you are providing the full DWI or just the b0 image in the input directory. That may be the issue.
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Meryam1985
commented
2 years ago Hello here is attached the full answer and error when I try to work without docker. Cordially.
Le vendredi 3 septembre 2021, 18:15:59 UTC+2, mabrouk Besma ***@***.***> a écrit : Hello here is attached the totality of the answer and error. also a screenshot of the files used. Cordially.
Le vendredi 3 septembre 2021, 17:12:25 UTC+2, Colin Hansen ***@***.***> a écrit : It looks like the epi_reg might have failed, but I can’t be sure without the full output log. Could you provide all of the output text in a txt file? That would make things easier. Also could you check if you are providing the full DWI or just the b0 image in the input directory. That may be the issue.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.
hanscol
commented
2 years ago For some reason I'm not seeing the attached files. If it is easier, you can email them to me directly hanscol45@gmail.com.
Hello I want to use MRTRIX3 to create the connectum of the DWI images. Converting the images I was using to BIDS format GIVEN:
Elapsed time (stage 2): 241.8
Total elapsed time: 299.3
Apply linear transform to T1 antsApplyTransforms -d 3 -i /tmp/tmp.RRepiyfNdY/T1_norm.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.RRepiyfNdY/ANTS0GenericAffine.mat -o /tmp/tmp.RRepiyfNdY/T1_norm_lin_atlas_2_5.nii.gz file /tmp/tmp.RRepiyfNdY/T1_norm.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(0x33c07c0): Input Primary is required but not set. /extra/prepare_input.sh: line 83: 744 Aborted (core dumped) antsApplyTransforms -d 3 -i /tmp/tmp.RRepiyfNdY/T1_norm.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.RRepiyfNdY/ANTS0GenericAffine.mat -o /tmp/tmp.RRepiyfNdY/T1_norm_lin_atlas_2_5.nii.gz
Apply linear transform to distorted b0 antsApplyTransforms -d 3 -i /INPUTS/b0.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.RRepiyfNdY/ANTS0GenericAffine.mat -t /tmp/tmp.RRepiyfNdY/epi_reg_d_ANTS.txt -o /tmp/tmp.RRepiyfNdY/b0_d_lin_atlas_2_5.nii.gz Transform file does not exist: /tmp/tmp.RRepiyfNdY/epi_reg_d_ANTS.txt
Apply nonlinear transform to T1 antsApplyTransforms -d 3 -i /tmp/tmp.RRepiyfNdY/T1_norm.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.RRepiyfNdY/ANTS1Warp.nii.gz -t /tmp/tmp.RRepiyfNdY/ANTS0GenericAffine.mat -o /tmp/tmp.RRepiyfNdY/T1_norm_nonlin_atlas_2_5.nii.gz file /tmp/tmp.RRepiyfNdY/T1_norm.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(0x37aecb0): Input Primary is required but not set. /extra/prepare_input.sh: line 99: 754 Aborted (core dumped) antsApplyTransforms -d 3 -i /tmp/tmp.RRepiyfNdY/T1_norm.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.RRepiyfNdY/ANTS1Warp.nii.gz -t /tmp/tmp.RRepiyfNdY/ANTS0GenericAffine.mat -o /tmp/tmp.RRepiyfNdY/T1_norm_nonlin_atlas_2_5.nii.gz
Apply nonlinear transform to distorted b0 antsApplyTransforms -d 3 -i /INPUTS/b0.nii.gz -r /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz -n BSpline -t /tmp/tmp.RRepiyfNdY/ANTS1Warp.nii.gz -t /tmp/tmp.RRepiyfNdY/ANTS0GenericAffine.mat -t /tmp/tmp.RRepiyfNdY/epi_reg_d_ANTS.txt -o /tmp/tmp.RRepiyfNdY/b0_d_nonlin_atlas_2_5.nii.gz Transform file does not exist: /tmp/tmp.RRepiyfNdY/epi_reg_d_ANTS.txt
knowing that I used the following acqparams.txt 0 1 0 0.034 0 1 0 0.000 with 0.034 is calculate by this way:1/BandwidthPerPixelPhaseEncode = 1/29.727 I would be grateful if someone can help me identify the error. cordially.