Hi Dr Yeh,
I have 2 issues faced:
1. I have removed the problematic volume and re-saved the SRC file. However, I tried running eddy correction via the command line interface with the updated SRC file but was still faced with the same error.
2. Is it possible to remove the problematic slice via CLI instead of on the GUI itself?
Steps that I did:
1. (on GUI) Step B1c: Dicom to SRC
2. (on GUI) Step T2: Removed problematic volume (removed row)
3. (on GUI) Step T2: Saved updated SRC file
3. (on CLI) Ran eddy correction on updated SRC file
Error: + [1;34mDSI Studio version: Chen"陳" command line [0m
| DSI Studio version: Chen"陳"
| action=rec
| source=C:\Users\vivien\Desktop\morn\20170523_F__019_S_4367\20170523_F__019_S_4367_s501_AxialDTI.src.gz
| loop=C:\Users\vivien\Desktop\morn\20170523_F__019_S_4367\20170523_F__019_S_4367_s501_AxialDTI.src.gz
| + [1;34mrun rec [0m
| | + [1;34mopen SRC file [0m
| | | + [1;34mopening 20170523_F__019_S_4367_s501_AxialDTI.src.gz [0m
| | | |_243 ms
| | |_297 ms
| | + [1;34mreconstruction parameters: [0m
| | | method=4
| | | odf_resolving=0
| | | record_odf=0
| | | dti_no_high_b=1
| | | check_btable=0
| | | other_output=fa,ad,rd,md,iso,rdi,nrdi
| | | r2_weighted=0
| | | thread_count=8
| | | param0=1.25
| | | param1=3000
| | | param2=0.05
| | | template 0:"ICBM152_adult.QA.nii"
| | | template 1:"C57BL6_mouse.QA.nii"
| | | template 2:"dHCP_neonate.QA.nii"
| | | template 3:"INDI_rhesus.QA.nii"
| | | template 4:"Pitt_marmoset.QA.nii"
| | | template 5:"WHS_SD_rat.QA.nii"
| | | template=0
| | |_3 ms
| | + [1;34mspecify mask [0m
| | | mask=1
| | |_1 ms
| | + [1;34mpreprocessing [0m
| | | preprocessing=0
| | | motion_correction=0
| | |_0 ms
| | + [1;34madditional processing steps [0m
| | | cmd=[Step T2][Corrections][EDDY]
| | | + [1;34m[Step T2][Corrections][EDDY] [0m
| | | | run eddy
| | | | eddy without topup
| | | | get the bounding box for speeding up topup/eddy
| | | | trim "20170523_F__019_S_4367_s501_AxialDTI.src.gz" for eddy
| | | | range: (0,0,0) to (128,128,80)
| | | | + [1;34msaving [0m
| | | | |_3.016 s
| | | | + [1;34msaving [0m
| | | | |_8 ms
| | | | run C:/Users/vivien/Desktop/dsi_studio_win_cpu/dsi_studio_win_cpu/plugin/eddy.exe
| | | | path:C:/Users/vivien/Desktop/morn/20170523_F__019_S_4367
| | | | --imain=20170523_F__019_S_4367_s501_AxialDTI.src.gz.nii.gz
| | | | --mask=20170523_F__019_S_4367_s501_AxialDTI.src.gz.mask.nii.gz
| | | | --acqp=20170523_F__019_S_4367_s501_AxialDTI.topup.acqparams.txt
| | | | --index=20170523_F__019_S_4367_s501_AxialDTI.src.gz.index.txt
| | | | --bvecs=20170523_F__019_S_4367_s501_AxialDTI.src.gz.bvec
| | | | --bvals=20170523_F__019_S_4367_s501_AxialDTI.src.gz.bval
| | | | --out=20170523_F__019_S_4367_s501_AxialDTI.src.gz.corrected
| | | | --verbose=1
| | | | eddy cannot process this data:Unknown error
| | | |_3.192 s
| | | [1;31mERROR:Unknown error [0m
| | |_3.193 s
| |_3.508 s
|_3.533 s