-save_src error

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Rory Piper

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Sep 26, 2022, 11:59:39 AMSep 26
to DSI Studio
Hi,

Please can I ask why this is happening? I am trrying to apply top-up with a reverse direction scan.

I get the following error: "Warning: --save_src is not used. Please check command line syntax." .......but I have specified a file location.


-------------------

rorypiper@MS00048528 dsi_test % dsi_studio --action=rec --source=src_folder/AP.src.gz --rev_pe=PA/sub-002_ses-7T_dir-PA_dwi.nii.gz --save_src=src_folder/topped.src.gz

+ DSI Studio version: Chen"陳" command line

| DSI Studio version: Chen"陳"

| action=rec

| source=src_folder/AP.src.gz

| + run rec

| | + open SRC file

| | | prepare index file for future accelerated loading

| | | + opening AP.src.gz

| | | |_2.945 s

| | | saving index file for accelerated loading: AP.src.gz.idx

| | |_3.425 s

| | + 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=12

| | | param0=1.25

| | | param1=3000

| | | param2=0.05

| | |_0 ms

| | + specify mask

| | | mask=1

| | |_0 ms

| | + preprocessing

| | | preprocessing=0

| | | rev_pe=PA/sub-002_ses-7T_dir-PA_dwi.nii.gz

| | | + run topup/eddy

| | | | + run topup

| | | | | + opening sub-002_ses-7T_dir-PA_dwi.nii.gz

| | | | | |_0 ms

| | | | | + reading image data

| | | | | |_25 ms

| | | | | projected correction:0.873243 0.894708 0 

| | | | | source com:100.143 125.536 78.2143 

| | | | | rev pe com:81.4865 63.5405 78.5405 

| | | | | source and reverse phase encoding: AP_PA

| | | | | create acq params at AP.topup.acqparams.txt

| | | | | 0 -1 0 0.05

| | | | | 0 1 0 0.05

| | | | | get the bounding box for speeding up topup/eddy

| | | | | create topup needed b0 nii.gz file from AP_PA b0

| | | | | + saving

| | | | | |_2.156 s

| | | | | FSL installation found at /usr/local/fsl

| | | | | run /usr/local/fsl/bin/topup

| | | | | path:/Users/rorypiper/Desktop/dsi_test/src_folder

| | | | | --warpres=20,16,14,12,10,6,4,4,4

| | | | | --subsamp=2,2,2,2,2,1,1,1,1

| | | | | --fwhm=8,6,4,3,3,2,1,0,0

| | | | | --miter=5,5,5,5,5,10,10,20,20

| | | | | --lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001

| | | | | --estmov=1,1,1,1,1,0,0,0,0

| | | | | --minmet=0,0,0,0,0,1,1,1,1

| | | | | --scale=1

| | | | | --imain=AP.topup.AP_PA.nii.gz

| | | | | --datain=AP.topup.acqparams.txt

| | | | | --out=AP

| | | | | --iout=AP.topup.check_result

| | | | | --verbose=1

| | | | |_2.387 s

| | | |_2.387 s

| | | ERROR:Unknown error

| | |_2.387 s

| |_5.95 s

|_5.954 s

Warning: --save_src is not used. Please check command line syntax.

Fang-Cheng Yeh

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Sep 26, 2022, 12:29:40 PMSep 26
to dsi-s...@googlegroups.com
The topup step failed.
Maybe you can try updating DSI Studio and see if it works (a certain version of DSI Studio has this problem).
If still does not work, please feel free to upload the data using the private upload link provided on the DSI Studio website.
Frank

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Rory Piper

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Sep 27, 2022, 10:34:41 AMSep 27
to DSI Studio
I was hoping that this is a simple/silly syntax error.

I am using Mac-12 version

Fang-Cheng Yeh

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Sep 27, 2022, 2:06:15 PMSep 27
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If you can upload the data, I can test on my side to figure out the problem.
Frank

Rory Piper

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Sep 28, 2022, 8:24:26 AMSep 28
to DSI Studio
Thanks Frank - I have uploaded this.

I have tried on a different subject on a Linux machine and I get the same error message about syntax.

Running in the GUI works fine, but I am keen to generate a script for this.

BW
Rory

Mengfei Cai

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Oct 30, 2022, 1:38:24 AMOct 30
to DSI Studio
Hi Frank

I have encountered the same issue on Ubuntu 2204 : [--save_src was not used].

"Running in the GUI works fine, but I am keen to generate a script for this." ----- it is also the case for me. I need to use CLI, not GUI.

Then I tried to download the latest version DSI_studio, it seems that the software package has some missing files after decompression.
The following files can only be found, not the [lib, plugins, doc, AppRun], could you check what's wrong?

  • color_map
  • atlas
  • LICENSE
  • dsi_studio
  • device.txt



Best
Mengfei

Fang-Cheng Yeh

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Oct 31, 2022, 10:52:05 AMOct 31
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Hi Rory,

     It worked on the Windows version.
     I would suggest updating DSI Studio or try it on GUI using [Step T2][Corrections][TOPUP EDDY] to see if the problem only exists in CLI.
     Another possibility is due to the installed FSL topup/eedy. You may also call them directly to rule out this possible cause.

Best,
Frank

+ [Step T2][Reconstruction]

| + open SRC file

| | prepare index file for future accelerated loading

| | + opening sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz

| | |_5.194 s

| | saving index file for accelerated loading: sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz.idx

| |_5.998 s

| change current directory to "E:/Dropbox/DSI Studio/Bug Report/Rory Piper - sub-02/ses-7T/dwi"

| + initiate interface

| |_43 ms

|_6.153 s

+ topup/eddy

| + [Step T2][Corrections][TOPUP EDDY]

| | param:E:/Dropbox/DSI Studio/Bug Report/Rory Piper - sub-02/ses-7T/dwi/sub-02_ses-7T_dir-PA_dwi.nii.gz

| | + run topup/eddy

| | | + run topup

| | | | + opening sub-02_ses-7T_dir-PA_dwi.nii.gz

| | | | |_0 ms

| | | | + reading image data

| | | | |_43 ms

| | | | projected correction:0.873243 0.894708 0

| | | | source com:100.143 125.536 78.2143

| | | | rev pe com:81.4865 63.5405 78.5405

| | | | source and reverse phase encoding: AP_PA

| | | | create acq params at sub-02_ses-7T_dir-AP_dwi.topup.acqparams.txt

| | | | 0 -1 0 0.05

| | | | 0 1 0 0.05

| | | | get the bounding box for speeding up topup/eddy

| | | | create topup needed b0 nii.gz file from AP_PA b0

| | | | + saving

| | | | |_3.376 s

| | | | run E:/Dropbox/work/GitHub/DSI-Studio-CMAKE/plugin/topup.exe

| | | | path:E:/Dropbox/DSI Studio/Bug Report/Rory Piper - sub-02/ses-7T/dwi

| | | | --warpres=20,16,14,12,10,6,4,4,4

| | | | --subsamp=2,2,2,2,2,1,1,1,1

| | | | --fwhm=8,6,4,3,3,2,1,0,0

| | | | --miter=5,5,5,5,5,10,10,20,20

| | | | --lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001

| | | | --estmov=1,1,1,1,1,0,0,0,0

| | | | --minmet=0,0,0,0,0,1,1,1,1

| | | | --scale=1

| | | | --imain=sub-02_ses-7T_dir-AP_dwi.topup.AP_PA.nii.gz

| | | | --datain=sub-02_ses-7T_dir-AP_dwi.topup.acqparams.txt

| | | | --out=sub-02_ses-7T_dir-AP_dwi

| | | | --iout=sub-02_ses-7T_dir-AP_dwi.topup.check_result

| | | | --verbose=1

| | | | SSD = 2259.18 n = 339480 Reg = 0 Cost = 2259.18

| | | | SSD = 893.199 n = 333178 Reg = 3.00153 Cost = 896.201

| | | | SSD = 536.266 n = 327374 Reg = 11.2481 Cost = 547.514

| | | | SSD = 510.943 n = 326373 Reg = 24.185 Cost = 535.128

| | | | SSD = 508.509 n = 326237 Reg = 26.4242 Cost = 534.933

| | | | SSD = 508.212 n = 326209 Reg = 26.7402 Cost = 534.952

| | | | SSD = 508.212 n = 326209 Reg = 26.74 Cost = 534.952

| | | | SSD = 508.214 n = 326209 Reg = 26.7386 Cost = 534.952

| | | | SSD = 508.225 n = 326209 Reg = 26.7275 Cost = 534.953

| | | | SSD = 508.308 n = 326213 Reg = 26.6437 Cost = 534.951

| | | | SSD = 508.434 n = 326228 Reg = 26.5043 Cost = 534.938

| | | | SSD = 508.494 n = 326237 Reg = 26.4371 Cost = 534.931

| | | | ***Going to next resolution level***

| | | | SSD = 775.17 n = 326237 Reg = 11.9375 Cost = 787.108

| | | | SSD = 672.722 n = 326197 Reg = 50.7154 Cost = 723.437

| | | | SSD = 629.155 n = 326167 Reg = 77.6483 Cost = 706.803

| | | | SSD = 616.437 n = 326144 Reg = 87.4403 Cost = 703.877

| | | | SSD = 612.972 n = 326134 Reg = 90.3199 Cost = 703.291

| | | | SSD = 612.046 n = 326129 Reg = 91.108 Cost = 703.154

| | | | ***Going to next resolution level***

| | | | SSD = 1089.38 n = 326129 Reg = 16.8247 Cost = 1106.2

| | | | SSD = 789.286 n = 326076 Reg = 76.8514 Cost = 866.137

| | | | SSD = 707.879 n = 326096 Reg = 114.481 Cost = 822.361

| | | | SSD = 686.783 n = 326102 Reg = 128.079 Cost = 814.863

| | | | SSD = 680.796 n = 326102 Reg = 132.386 Cost = 813.182

| | | | SSD = 678.889 n = 326100 Reg = 133.827 Cost = 812.716

| | | | ***Going to next resolution level***

| | | | SSD = 1080.47 n = 326100 Reg = 35.6966 Cost = 1116.16

| | | | SSD = 845.794 n = 326065 Reg = 84.0278 Cost = 929.822

| | | | SSD = 784.87 n = 326054 Reg = 115.511 Cost = 900.381

| | | | SSD = 770.628 n = 326053 Reg = 125.371 Cost = 895.999

| | | | SSD = 766.942 n = 326055 Reg = 128.088 Cost = 895.03

| | | | SSD = 765.826 n = 326055 Reg = 128.928 Cost = 894.755

| | | | ***Going to next resolution level***

| | | | SSD = 768.115 n = 326055 Reg = 49.9405 Cost = 818.055

| | | | SSD = 635.271 n = 326040 Reg = 68.6422 Cost = 703.913

| | | | SSD = 597.359 n = 326028 Reg = 87.3756 Cost = 684.734

| | | | SSD = 589.588 n = 326028 Reg = 93.0121 Cost = 682.6

| | | | SSD = 588.055 n = 326015 Reg = 94.2495 Cost = 682.305

| | | | SSD = 587.678 n = 326015 Reg = 94.552 Cost = 682.23

| | | | ***Going to next resolution level***

| | | | SSD = 1109.22 n = 2675473 Reg = 156.093 Cost = 1265.31

| | | | SSD = 1099.48 n = 2675473 Reg = 154.865 Cost = 1254.35

| | | | SSD = 1082.98 n = 2675473 Reg = 152.888 Cost = 1235.87

| | | | SSD = 1057.46 n = 2675473 Reg = 150.13 Cost = 1207.59

| | | | SSD = 1021.6 n = 2675473 Reg = 146.977 Cost = 1168.58

| | | | SSD = 976.325 n = 2675473 Reg = 144.382 Cost = 1120.71

| | | | SSD = 925.423 n = 2675473 Reg = 143.764 Cost = 1069.19

| | | | SSD = 896.212 n = 2675473 Reg = 145.702 Cost = 1041.91

| | | | SSD = 861.169 n = 2675473 Reg = 149.762 Cost = 1010.93

| | | | SSD = 824.171 n = 2675473 Reg = 158.793 Cost = 982.964

| | | | SSD = 808.369 n = 2675473 Reg = 164.362 Cost = 972.731

| | | | ***Going to next resolution level***

| | | | SSD = 2175.4 n = 2675473 Reg = 60.6203 Cost = 2236.02

| | | | SSD = 2152.24 n = 2675473 Reg = 60.339 Cost = 2212.58

| | | | SSD = 2112.17 n = 2675473 Reg = 59.9631 Cost = 2172.14

| | | | SSD = 2049.25 n = 2675473 Reg = 59.7035 Cost = 2108.96

| | | | SSD = 1961.16 n = 2675473 Reg = 60.1631 Cost = 2021.32

| | | | SSD = 1850.29 n = 2675473 Reg = 62.3702 Cost = 1912.66

| | | | SSD = 1723.93 n = 2675473 Reg = 67.6452 Cost = 1791.58

| | | | SSD = 1626.3 n = 2675473 Reg = 75.4706 Cost = 1701.77

| | | | SSD = 1571.17 n = 2675473 Reg = 81.2855 Cost = 1652.45

| | | | SSD = 1475.99 n = 2675473 Reg = 98.1373 Cost = 1574.13

| | | | SSD = 1438.81 n = 2675473 Reg = 106.995 Cost = 1545.8

| | | | ***Going to next resolution level***

| | | | SSD = 1631.92 n = 2675473 Reg = 1.21355 Cost = 1633.13

| | | | SSD = 1629.4 n = 2675473 Reg = 1.21406 Cost = 1630.62

| | | | SSD = 1626 n = 2675473 Reg = 1.21596 Cost = 1627.22

| | | | SSD = 1621.68 n = 2675473 Reg = 1.22132 Cost = 1622.9

| | | | SSD = 1614.5 n = 2675473 Reg = 1.23508 Cost = 1615.74

| | | | SSD = 1601.04 n = 2675473 Reg = 1.26361 Cost = 1602.31

| | | | SSD = 1583.2 n = 2675473 Reg = 1.31013 Cost = 1584.51

| | | | SSD = 1567.46 n = 2675473 Reg = 1.35676 Cost = 1568.82

| | | | SSD = 1524.65 n = 2675473 Reg = 1.51041 Cost = 1526.16

| | | | SSD = 1492.71 n = 2675473 Reg = 1.67529 Cost = 1494.39

| | | | SSD = 1442.47 n = 2675473 Reg = 2.0596 Cost = 1444.53

| | | | SSD = 1425.28 n = 2675473 Reg = 2.28001 Cost = 1427.56

| | | | SSD = 1404.92 n = 2675473 Reg = 2.70885 Cost = 1407.63

| | | | SSD = 1397.47 n = 2675473 Reg = 2.87939 Cost = 1400.35

| | | | SSD = 1385.07 n = 2675473 Reg = 3.24545 Cost = 1388.32

| | | | SSD = 1372.34 n = 2675473 Reg = 3.63012 Cost = 1375.97

| | | | SSD = 1366.47 n = 2675473 Reg = 3.82119 Cost = 1370.29

| | | | SSD = 1356.51 n = 2675473 Reg = 4.10708 Cost = 1360.62

| | | | SSD = 1345.77 n = 2675473 Reg = 4.4295 Cost = 1350.2

| | | | SSD = 1340.14 n = 2675473 Reg = 4.58775 Cost = 1344.72

| | | | SSD = 1332.42 n = 2675473 Reg = 4.79752 Cost = 1337.22

| | | | ***Going to next resolution level***

| | | | SSD = 1332.42 n = 2675473 Reg = 0.0959504 Cost = 1332.51

| | | | SSD = 1331.36 n = 2675473 Reg = 0.0958471 Cost = 1331.46

| | | | SSD = 1330.03 n = 2675473 Reg = 0.0957015 Cost = 1330.13

| | | | SSD = 1328.51 n = 2675473 Reg = 0.0954957 Cost = 1328.6

| | | | SSD = 1326.24 n = 2675473 Reg = 0.0951166 Cost = 1326.34

| | | | SSD = 1322.05 n = 2675473 Reg = 0.0943555 Cost = 1322.14

| | | | SSD = 1316.67 n = 2675473 Reg = 0.0932915 Cost = 1316.76

| | | | SSD = 1312.38 n = 2675473 Reg = 0.0924245 Cost = 1312.47

| | | | SSD = 1299.99 n = 2675473 Reg = 0.0898902 Cost = 1300.08

| | | | SSD = 1293.09 n = 2675473 Reg = 0.0882993 Cost = 1293.18

| | | | SSD = 1280.42 n = 2675473 Reg = 0.085186 Cost = 1280.5

| | | | SSD = 1276.29 n = 2675473 Reg = 0.0839897 Cost = 1276.37

| | | | SSD = 1271.61 n = 2675473 Reg = 0.0823922 Cost = 1271.69

| | | | SSD = 1269.51 n = 2675473 Reg = 0.0817834 Cost = 1269.59

| | | | SSD = 1267.34 n = 2675473 Reg = 0.0814063 Cost = 1267.43

| | | | SSD = 1265.3 n = 2675473 Reg = 0.0813944 Cost = 1265.38

| | | | SSD = 1263.59 n = 2675473 Reg = 0.0818962 Cost = 1263.67

| | | | SSD = 1261.84 n = 2675473 Reg = 0.0830398 Cost = 1261.92

| | | | SSD = 1258.54 n = 2675473 Reg = 0.0863478 Cost = 1258.62

| | | | SSD = 1256.87 n = 2675473 Reg = 0.0883106 Cost = 1256.96

| | | | SSD = 1252.74 n = 2675473 Reg = 0.0944434 Cost = 1252.83

| | | | completed.

| | | |_13.4103 m

| | | run eddy

| | | trim "sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz" for eddy

| | | range: (0,0,0) to (184,164,96)

| | | + saving

| | | |_1.84035 m

| | | + saving

| | | |_76 ms

| | | run E:/Dropbox/work/GitHub/DSI-Studio-CMAKE/plugin/eddy_cuda.exe

| | | path:E:/Dropbox/DSI Studio/Bug Report/Rory Piper - sub-02/ses-7T/dwi

| | | --imain=sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz.nii.gz

| | | --mask=sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz.mask.nii.gz

| | | --acqp=sub-02_ses-7T_dir-AP_dwi.topup.acqparams.txt

| | | --index=sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz.index.txt

| | | --bvecs=sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz.bvec

| | | --bvals=sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz.bval

| | | --out=sub-02_ses-7T_dir-AP_dwi.nii.gz.src.gz.corrected

| | | --verbose=1

| | | --topup=sub-02_ses-7T_dir-AP_dwi

| | | Reading images

| | | Performing volume-to-volume registration

| | | Running Register

| | | ...................Allocated GPU # 0...................

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 0, Total mss = 1693.9

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 1, Total mss = 1231.36

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 2, Total mss = 562.552

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 3, Total mss = 437.061

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 4, Total mss = 395.617

| | | Running sm.ApplyB0LocationReference

| | | Running sm.PolateB0MovPar

| | | Running Register

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Checking for outliers

| | | Calculating parameter updates


Fang-Cheng Yeh

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Oct 31, 2022, 10:53:44 AMOct 31
to dsi-s...@googlegroups.com
Hi Mengfei,

     If you are using the Linux version, then there won't be the same folders as in Mac or Windows. DSI Studio will call the installed FSL.

     You may also post the CLI command you used and the log output to help identify the issue.

Best regards,
Frank

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