(CLI) eddy cannot process this data:Unknown error

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vivien

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Jan 5, 2023, 5:02:48 AM1/5/23
to DSI Studio
Hi Dr Yeh, 

I have tried running eddy correction via the command line interface but was faced with this error (pasted below). I tried running eddy with the same src file in the GUI and it works. 

I ran the command below: 
path=C:\Users\vivien\Desktop\dsi_studio_win_cpu\dsi_studio_win_cpu
dsi_studio --action=rec --source=C:\Users\vivien\Desktop\cml\20170523_F__019_S_4367\20170523_F__019_S_4367_s501_AxialDTI.src.gz --cmd="[Step T2][Corrections][EDDY]" --method=4 --param0=1.25 > log.txt


I have uploaded the SRC file in dropbox for you titled: 20170523_F__019_S_4367_s501_AxialDTI.src.gz

+ [1;34mDSI Studio version: Chen"陳" command line [0m
| DSI Studio version: Chen"陳"
| action=rec
| source=C:\Users\vivien\Desktop\20170523_F__019_S_4367_s501_AxialDTI.src.gz
| loop=C:\Users\vivien\Desktop\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
| | | |_229 ms
| | |_275 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
| | |_2 ms
| | + [1;34mspecify mask [0m
| | | mask=1
| | |_0 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
| | | | |_2.78 s
| | | | + [1;34msaving [0m
| | | | |_6 ms
| | | | run C:/Users/vivien/Desktop/dsi_studio_win_cpu/dsi_studio_win_cpu/plugin/eddy.exe
| | | | path:C:/Users/vivien/Desktop
| | | | --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
| | | |_2.906 s
| | | [1;31mERROR:Unknown error [0m
| | |_2.906 s
| |_3.194 s
|_3.205 s





Fang-Cheng Yeh

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Jan 5, 2023, 10:25:05 AM1/5/23
to dsi-s...@googlegroups.com
Sorry for the issue.

I will check and get back to you soon
Frank

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Fang-Cheng Yeh

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Jan 10, 2023, 8:20:54 PM1/10/23
to dsi-s...@googlegroups.com
There is a problematic volume in the SRC file. 
You will need to re-create the SRC file or remove it (the 34th DWI's b vector is zero. It can be removed at Step T2).

image.png
Frank

vivien

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Jan 11, 2023, 6:36:33 PM1/11/23
to DSI Studio
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.
 Capture.JPG

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


Thank you!

Fang-Cheng Yeh

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Jan 11, 2023, 6:51:51 PM1/11/23
to dsi-s...@googlegroups.com
Removing the problematic volume worked on my side. Could you try download the current version of DSIStudio? You may tru the GPU and CPU version to see which one works.
Frank

vivien

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Jan 18, 2023, 1:38:31 AM1/18/23
to DSI Studio
Hi Dr Yeh,

I re-downloaded DSIStudio recommended GPU version and tried. With the removed problematic volume src file, it works on GUI but running Eddy Correction via the command line still shows the same error. 

Fang-Cheng Yeh

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Jan 22, 2023, 9:17:26 PM1/22/23
to dsi-s...@googlegroups.com
I created a new SRC with the last b0 removed and run CLI: --action=rec --source=AxialDTI.src.gz --cmd="[Step T2][Corrections][EDDY]" --method=4 --param0=1.25

It works:

source=AxialDTI.src.gz
action=rec
loop=AxialDTI.src.gz
+ run rec
| + open SRC file
| | + opening AxialDTI.src.gz
| | |_341 ms
| |_417 ms
| + reconstruction parameters:

| | 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=40

| | 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
| |_41 ms
| + specify mask
| | mask=1
| |_1 ms
| + preprocessing
| | preprocessing=0
| | motion_correction=0
| |_1 ms
| + additional processing steps

| | cmd=[Step T2][Corrections][EDDY]
| | + [Step T2][Corrections][EDDY]

| | | run eddy
| | | eddy without topup
| | | get the bounding box for speeding up topup/eddy
| | | trim "AxialDTI.src.gz" for eddy
| | | range: (0,0,0) to (128,128,80)
| | | + saving
| | | |_3.638 s
| | | + saving
| | | |_9 ms
| | | run E:/Dropbox/work/GitHub/DSI-Studio-CMAKE/plugin/eddy_cuda.exe
| | | path:D:/
| | | --imain=AxialDTI.src.gz.nii.gz
| | | --mask=AxialDTI.src.gz.mask.nii.gz
| | | --acqp=AxialDTI.topup.acqparams.txt
| | | --index=AxialDTI.src.gz.index.txt
| | | --bvecs=AxialDTI.src.gz.bvec
| | | --bvals=AxialDTI.src.gz.bval
| | | --out=AxialDTI.src.gz.corrected
| | | --verbose=1
| | | Reading images
| | | Performing volume-to-volume registration
| | | Running Register
| | | ...................Allocated GPU # 0...................
| | | Loading prediction maker
| | | Evaluating prediction maker model
| | | Checking for outliers
| | | Calculating parameter updates

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