Dear mrtrix experts,
I’ve been trying to run the dwifslpreproc step, and I found a defect in the output image. I used the command:
dwifslpreproc dwi_den_unr.nii.gz dwi2_den_unr_preproc.nii.gz -rpe_none -pe_dir AP -fslgrad DTI.bvec DTI.bval -eddy_options " --slm=linear" -info
I didn’t encounter any errors or warnings during the step.however, it was found that part of the output image was cut.
here is the log:
dwifslpreproc:
dwifslpreproc: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwifslpreproc:
dwifslpreproc: Loading header for image file '/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwi_den_unr.nii.gz'
dwifslpreproc: Generated scratch directory: /n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwifslpreproc-tmp-GYN6AX/
Command: mrconvert /n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwi_den_unr.nii.gz /n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwifslpreproc-tmp-GYN6AX/dwi.mif -fslgrad /n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/DTI.bvec /n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/DTI.bval -json_export /n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwifslpreproc-tmp-GYN6AX/dwi.json
mrconvert: [ 0%] uncompressing image "/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwi_den mrconvert: [100%] uncompressing image "/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwi_den_unr.nii.gz"
mrconvert: [ 0%] copying from "/n01dat01/...rotation/dwi_den_unr.nii.gz" to "/n01dat01/...lpreproc- mrconvert: [100%] copying from "/n01dat01/...rotation/dwi_den_unr.nii.gz" to "/n01dat01/...lpreproc-tmp-GYN6AX/dwi.mif"
dwifslpreproc: Changing to scratch directory (/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwifslpreproc-tmp-GYN6AX/)
dwifslpreproc: Loading header for image file 'dwi.mif'
dwifslpreproc: Command: '/n10dat01/yhlu/local/mrtrix3/bin/mrinfo dwi.mif -shell_indices' (piping data to local storage)
dwifslpreproc: Result: 0 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64 65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128
dwifslpreproc: Total readout time not provided at command-line; assuming sane default of 0.1
Command: mrinfo dwi.mif -export_grad_mrtrix grad.b
Command: dwi2mask dwi.mif - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -strides -1,+2,+3
dwi2mask: [100%] preloading data for "dwi.mif"
dwi2mask: [done] computing dwi brain mask
dwi2mask: [done] applying mask cleaning filter
maskfilter: [100%] applying dilate filter to image -
mrconvert: [100%] copying from "/n01dat01/...YN6AX/mrtrix-tmp-CNtHUN.mif" to "eddy_mask.nii"
Command: mrconvert dwi.mif -import_pe_table dwi_manual_pe_scheme.txt eddy_in.nii -strides -1,+2,+3,+4 -export_grad_fsl bvecs bvals -export_pe_eddy eddy_config.txt eddy_indices.txt
mrconvert: [100%] copying from "dwi.mif" to "eddy_in.nii"
Command: eddy_cuda9.1 --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --slm=linear --out=dwi_post_eddy --verbose
dwifslpreproc: CUDA version of 'eddy' was not successful; attempting OpenMP version
Command: eddy_openmp --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --slm=linear --out=dwi_post_eddy --verbose
dwifslpreproc: Output of eddy command:
Reading images
Performing volume-to-volume registration
Running Register
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 7.522186
0.108371
1.233575
7.958603
-4.766802
Calculating parameter updates
Iter: 0, Total mss = 0.865743
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 3.844992
0.103310
1.196333
3.991229
3.029630
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 4.457266
0.115941
1.272207
4.679263
1.771811
Calculating parameter updates
Iter: 1, Total mss = 0.818615
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 4.446353
0.116927
1.230729
4.675287
2.469645
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 3.913006
0.091492
1.187898
4.267419
2.761091
Calculating parameter updates
Iter: 2, Total mss = 0.941769
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 4.133000
-0.060859
0.955434
4.833008
3.056813
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 4.190730
0.062678
1.067648
4.602773
2.546743
Calculating parameter updates
Iter: 3, Total mss = 0.778839
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 4.213829
-0.086052
0.915743
4.946187
3.145770
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 3.921278
-0.054459
0.810168
4.707138
3.104814
Calculating parameter updates
Iter: 4, Total mss = 0.874511
Running sm.ApplyDWILocationReference
Checking shell alignment along PE-direction (running PostEddyAlignShellsAlongPE)
Aligning shells (running PostEddyAlignShells)
Performing final outlier check
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 3.629466
0.151540
0.320865
2.462734
0.759607
Running sm.WriteParameterFile
Running sm.WriteRegisteredImages
Running sm.RecycleOutliers
Running sm.WriteRotatedBVecs
Running sm.WriteMovementRMS
Command: mrconvert dwi_post_eddy.nii.gz result.mif -strides 1,2,3,4 -fslgrad dwi_post_eddy.eddy_rotated_bvecs bvals
mrconvert: [100%] uncompressing image "dwi_post_eddy.nii.gz"
mrconvert: [100%] copying from "dwi_post_eddy.nii.gz" to "result.mif"
dwifslpreproc: Loading header for image file 'result.mif'
Command: mrconvert result.mif /n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwi2_den_unr_preproc.nii.gz
mrconvert: [100%] copying from "result.mif" to "/n01dat01/...dwi2_den_unr_preproc.nii.gz"
mrconvert: [ 0%] compressing image "/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwi2_den_ mrconvert: [100%] compressing image "/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwi2_den_unr_preproc.nii.gz"
dwifslpreproc: Changing back to original directory (/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation)
dwifslpreproc: Deleting scratch directory (/n01dat01/yfliu/TianYaru_2020/00_DATA/M02/02_rotation/dwifslpreproc-tmp-GYN6AX/)
here are input image and out put image:
Thank you for any tips in advance.
Regards,
Jade