-save_src error

Rory Piper

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Sep 26, 2022, 11:59:39 AM9/26/22

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

| | | | | |_25 ms

| | | | | 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

| | | | | |_2.156 s

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

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

| | | | |_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 PM9/26/22

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 AM9/27/22

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 PM9/27/22

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If you can upload the data, I can test on my side to figure out the problem.

Frank

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/3b818249-01be-4422-a638-78206c59e090n%40googlegroups.com.

Rory Piper

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Sep 28, 2022, 8:24:26 AM9/28/22

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 AM10/30/22

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 AM10/31/22

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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

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/72e62148-4ecc-4351-ab60-fa354c8372afn%40googlegroups.com.

Fang-Cheng Yeh

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Oct 31, 2022, 10:53:44 AM10/31/22

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

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/247a8785-2fcc-461e-85de-32d38b5be9aan%40googlegroups.com.

Ida R.

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Mar 17, 2024, 11:52:45 PMMar 17

to DSI Studio

Hi Frank,

I've encountered the same problem with "--save_src is not used/recognized" while using a batch script in Matlab. I wondered if there has been any recent developments? I am using Mac OS Sonoma 14.4 and Matlab 2023b. It works normally when I use the GUI, but it would be much more efficient if I could run everything through a Matlab batch script.

This is the command line that is causing problems:

cmd = sprintf('%s --action=rec --source=%s --rev_pe=%s --save_src=%s', ...

DSI_exec, src_file, rev_pe_image, processed_src_file);

system(cmd);

| | | | | 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

Ida

Frank Yeh

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Mar 18, 2024, 11:03:09 AMMar 18

to rangu...@gmail.com, DSI Studio

TOPUP or eddy crashed before saving the SRC file.

Could you list the console output from GUI? (click on the console button). There may be a hint for the differences.

Alternatively, you may use GUI to batch process all data. Just select all SRC files and see if DSI Studio works out for them. It will try to figure out the corresponding AP-PA file combination if they have a similar naming pattern.

Best,

Frank

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/c155ff5e-b3c4-43e5-b3d6-b8526084a3d9n%40googlegroups.com.

Ida R.

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Mar 18, 2024, 11:32:11 AMMar 18

to DSI Studio

Thank you, this is the GUI output (different participant now, but all subfolders are structured the same. Also I added the T1w for a QSDR rec at a later stage):

the DSI_exec command I am using is DSI_exec = "/Applications/dsi_studio.app/Contents/MacOS/dsi_studio" I was wondering whether it should be "/Applications/dsi_studio.app/Contents/MacOS/plugin/topup" for this particular task (given the information from the GUI output).

DSI Studio version: Chen"陳" Feb 5 2024

| DSI Studio version: Chen"陳"

|_6 ms

[Step T2][Reconstruction]

|-open SRC file DTI_20191211130957_12_dwi_AP.nii.src.gz

| | generating mask

| |_471 ms

| change current directory to "/Volumes/T7/ABCDTI2/ABC1023/ABC"

|-initiate interface

| |_5 ms

|_524 ms

add /Volumes/T7/ABCDTI2/ABC1023/ABC/T1_20191211130957_09_anat_T1w.nii as T1_20191211130957_09_anat_T1w and register image with DWI.

translocation: -0.618254 1.49249 -5.98218

rotation: 0.234337 0 0

scaling: 1 1 1

shear: 0 0 0

[Step T2][Corrections][TOPUP EDDY]

| param: /Volumes/T7/ABCDTI2/ABC1023/ABC/DTIrev_20191211130957_14_dwi_rev.nii

|-run topup/eddy

| |-run topup

| | | projected correction: 0.903247 0.998147 0

| | | source com: 47.2727 53.0909 38.9091

| | | rev pe com: 49.2319 20.5942 7.78261

| | | source and reverse phase encoding: AP_PA

| | | create acq params at DTI_20191211130957_12_dwi_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

| | | run /Applications/dsi_studio.app/Contents/MacOS/plugin/topup

| | | path: /Volumes/T7/ABCDTI2/ABC1023/ABC

| | | --imain=DTI_20191211130957_12_dwi_AP.topup.AP_PA.nii.gz

| | | --datain=DTI_20191211130957_12_dwi_AP.topup.acqparams.txt

| | | --out=DTI_20191211130957_12_dwi_AP

| | | --iout=DTI_20191211130957_12_dwi_AP.topup.check_result

| | | --verbose=1

| | | --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

| | | --ssqlambda=1

| | | --regmod=bending_energy

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

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

| | | --splineorder=3

| | | --numprec=double

| | | --interp=spline

| | | --scale=1

| | |-calling external program

| | | | SSD = 1066.64 n = 35991 Reg = 0 Cost = 1066.64

| | | | SSD = 616.466 n = 35991 Reg = 42.5688 Cost = 659.035

| | | | SSD = 507.976 n = 35991 Reg = 83.9283 Cost = 591.905

| | | | SSD = 478.809 n = 35991 Reg = 101.256 Cost = 580.065

| | | | SSD = 469.61 n = 35991 Reg = 107.412 Cost = 577.022

| | | | SSD = 466.414 n = 35991 Reg = 109.667 Cost = 576.081

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

| | | | SSD = 710.8 n = 35991 Reg = 40.9368 Cost = 751.737

| | | | SSD = 507.743 n = 35991 Reg = 86.2502 Cost = 593.993

| | | | SSD = 433.969 n = 35991 Reg = 118.167 Cost = 552.136

| | | | SSD = 407.167 n = 35991 Reg = 132.33 Cost = 539.497

| | | | SSD = 396.576 n = 35991 Reg = 138.444 Cost = 535.021

| | | | SSD = 392.147 n = 35991 Reg = 141.116 Cost = 533.263

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

| | | | SSD = 883.237 n = 35991 Reg = 42.7744 Cost = 926.011

| | | | SSD = 565.992 n = 35991 Reg = 69.1695 Cost = 635.162

| | | | SSD = 483.618 n = 35991 Reg = 94.5092 Cost = 578.128

| | | | SSD = 457.998 n = 35991 Reg = 106.039 Cost = 564.036

| | | | SSD = 448.704 n = 35991 Reg = 110.905 Cost = 559.609

| | | | SSD = 444.672 n = 35991 Reg = 113.157 Cost = 557.829

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

| | | | SSD = 613.194 n = 35991 Reg = 23.3332 Cost = 636.527

| | | | SSD = 532.747 n = 35991 Reg = 41.0975 Cost = 573.845

| | | | SSD = 502.767 n = 35991 Reg = 53.3276 Cost = 556.094

| | | | SSD = 493.584 n = 35991 Reg = 58.5208 Cost = 552.104

| | | | SSD = 490.061 n = 35991 Reg = 60.7461 Cost = 550.807

| | | | SSD = 488.126 n = 35991 Reg = 62.0219 Cost = 550.148

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

| | | | SSD = 487.669 n = 35991 Reg = 24.3592 Cost = 512.028

| | | | SSD = 322.971 n = 35991 Reg = 21.1883 Cost = 344.159

| | | | SSD = 284.765 n = 35991 Reg = 27.9978 Cost = 312.763

| | | | SSD = 277.442 n = 35991 Reg = 31.0788 Cost = 308.521

| | | | SSD = 275.2 n = 35991 Reg = 32.1808 Cost = 307.381

| | | | SSD = 274.009 n = 35991 Reg = 32.7312 Cost = 306.74

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

| | | | SSD = 942.824 n = 301906 Reg = 167.021 Cost = 1109.85

| | | | SSD = 914.251 n = 301906 Reg = 161.833 Cost = 1076.08

| | | | SSD = 873.9 n = 301906 Reg = 154.502 Cost = 1028.4

| | | | SSD = 824.035 n = 301906 Reg = 145.433 Cost = 969.468

| | | | SSD = 766.26 n = 301906 Reg = 134.939 Cost = 901.199

| | | | SSD = 707.039 n = 301906 Reg = 124.286 Cost = 831.326

| | | | SSD = 677.994 n = 301906 Reg = 119.02 Cost = 797.014

| | | | SSD = 636.993 n = 301906 Reg = 111.871 Cost = 748.864

| | | | SSD = 605.208 n = 301906 Reg = 106.527 Cost = 711.734

| | | | SSD = 584.137 n = 301906 Reg = 103.093 Cost = 687.23

| | | | SSD = 563.175 n = 301906 Reg = 99.8457 Cost = 663.021

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

| | | | SSD = 763.902 n = 301906 Reg = 15.9905 Cost = 779.892

| | | | SSD = 756.941 n = 301906 Reg = 15.8466 Cost = 772.788

| | | | SSD = 745.303 n = 301906 Reg = 15.6079 Cost = 760.911

| | | | SSD = 726.334 n = 301906 Reg = 15.224 Cost = 741.558

| | | | SSD = 697.522 n = 301906 Reg = 14.6561 Cost = 712.179

| | | | SSD = 658.533 n = 301906 Reg = 13.926 Cost = 672.459

| | | | SSD = 634.792 n = 301906 Reg = 13.5241 Cost = 648.316

| | | | SSD = 592.761 n = 301906 Reg = 12.8465 Cost = 605.608

| | | | SSD = 555.778 n = 301906 Reg = 12.378 Cost = 568.156

| | | | SSD = 528.724 n = 301906 Reg = 12.174 Cost = 540.898

| | | | SSD = 508.088 n = 301906 Reg = 12.197 Cost = 520.285

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

| | | | SSD = 508.106 n = 301906 Reg = 0.121974 Cost = 508.228

| | | | SSD = 506.354 n = 301906 Reg = 0.12155 Cost = 506.475

| | | | SSD = 504.367 n = 301906 Reg = 0.12107 Cost = 504.488

| | | | SSD = 501.778 n = 301906 Reg = 0.120455 Cost = 501.899

| | | | SSD = 497.131 n = 301906 Reg = 0.119389 Cost = 497.251

| | | | SSD = 490.342 n = 301906 Reg = 0.11796 Cost = 490.46

| | | | SSD = 486.305 n = 301906 Reg = 0.117285 Cost = 486.422

| | | | SSD = 475.868 n = 301906 Reg = 0.115621 Cost = 475.983

| | | | SSD = 467.41 n = 301906 Reg = 0.114846 Cost = 467.525

| | | | SSD = 453.964 n = 301906 Reg = 0.114485 Cost = 454.078

| | | | SSD = 443.652 n = 301906 Reg = 0.11574 Cost = 443.768

| | | | SSD = 430.442 n = 301906 Reg = 0.11964 Cost = 430.562

| | | | SSD = 423.483 n = 301906 Reg = 0.123956 Cost = 423.607

| | | | SSD = 416.797 n = 301906 Reg = 0.130137 Cost = 416.927

| | | | SSD = 413.017 n = 301906 Reg = 0.13454 Cost = 413.151

| | | | SSD = 409.107 n = 301906 Reg = 0.139386 Cost = 409.246

| | | | SSD = 406.307 n = 301906 Reg = 0.142905 Cost = 406.45

| | | | SSD = 403.294 n = 301906 Reg = 0.146438 Cost = 403.441

| | | | SSD = 400.394 n = 301906 Reg = 0.149432 Cost = 400.543

| | | | SSD = 397.021 n = 301906 Reg = 0.152629 Cost = 397.174

| | | | SSD = 393.593 n = 301906 Reg = 0.155611 Cost = 393.749

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

| | | | SSD = 393.593 n = 301906 Reg = 0.00311222 Cost = 393.596

| | | | SSD = 393.05 n = 301906 Reg = 0.00310701 Cost = 393.053

| | | | SSD = 392.335 n = 301906 Reg = 0.00309959 Cost = 392.339

| | | | SSD = 391.221 n = 301906 Reg = 0.00308703 Cost = 391.224

| | | | SSD = 389.212 n = 301906 Reg = 0.00306375 Cost = 389.215

| | | | SSD = 386.341 n = 301906 Reg = 0.00302907 Cost = 386.344

| | | | SSD = 384.649 n = 301906 Reg = 0.00300695 Cost = 384.652

| | | | SSD = 379.792 n = 301906 Reg = 0.00294428 Cost = 379.795

| | | | SSD = 377.011 n = 301906 Reg = 0.0029039 Cost = 377.014

| | | | SSD = 372.398 n = 301906 Reg = 0.00283313 Cost = 372.4

| | | | SSD = 370.221 n = 301906 Reg = 0.00279424 Cost = 370.224

| | | | SSD = 367.339 n = 301906 Reg = 0.00273971 Cost = 367.342

| | | | SSD = 365.653 n = 301906 Reg = 0.00270802 Cost = 365.655

| | | | SSD = 363.525 n = 301906 Reg = 0.00267299 Cost = 363.528

| | | | SSD = 362.296 n = 301906 Reg = 0.00265804 Cost = 362.299

| | | | SSD = 361.217 n = 301906 Reg = 0.00265191 Cost = 361.219

| | | | SSD = 360.399 n = 301906 Reg = 0.00265354 Cost = 360.402

| | | | SSD = 359.715 n = 301906 Reg = 0.00266193 Cost = 359.718

| | | | SSD = 358.902 n = 301906 Reg = 0.00267859 Cost = 358.905

| | | | SSD = 358.09 n = 301906 Reg = 0.00270303 Cost = 358.093

| | | | completed.

| | | |_41.284 s

| | |_44.55 s

| | run eddy

| |-saving results

| | | trim "DTI_20191211130957_12_dwi_AP.nii.src.gz" for eddy

| | | range: (18,8,0) to (84,94,58)

| | |_3.191 s

| | run /Applications/dsi_studio.app/Contents/MacOS/plugin/eddy

| | path: /Volumes/T7/ABCDTI2/ABC1023/ABC

| | --imain=DTI_20191211130957_12_dwi_AP.nii.src.gz.nii.gz

| | --mask=DTI_20191211130957_12_dwi_AP.nii.src.gz.mask.nii.gz

| | --acqp=DTI_20191211130957_12_dwi_AP.topup.acqparams.txt

| | --index=DTI_20191211130957_12_dwi_AP.nii.src.gz.index.txt

| | --bvecs=DTI_20191211130957_12_dwi_AP.nii.src.gz.bvec

| | --bvals=DTI_20191211130957_12_dwi_AP.nii.src.gz.bval

| | --out=DTI_20191211130957_12_dwi_AP.nii.src.gz.corrected

| | --verbose=1

| | --topup=DTI_20191211130957_12_dwi_AP

| |-calling external program

| | | Reading images

| | | Performing volume-to-volume registration

| | | Running Register

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 0, Total mss = 231.445

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 1, Total mss = 186.249

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 2, Total mss = 183.63

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 3, Total mss = 183.158

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Calculating parameter updates

| | | Iter: 4, Total mss = 183.081

| | | Running sm.ApplyB0LocationReference

| | | Running sm.PolateB0MovPar

| | | Running Register

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 0.401276

| | | 0.489148

| | | 8.416793

| | | 2.762865

| | | 2.305799

| | | Calculating parameter updates

| | | Iter: 0, Total mss = 15770596.659918

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 2.425507

| | | 0.481635

| | | 7.854293

| | | 4.806594

| | | 4.367612

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 0.815294

| | | 0.477904

| | | 8.031752

| | | 3.160685

| | | 2.697412

| | | Calculating parameter updates

| | | Iter: 1, Total mss = 10.176313

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 0.931177

| | | 0.441119

| | | 7.035581

| | | 3.610927

| | | 3.305674

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: -0.520419

| | | 0.459068

| | | 6.993822

| | | 2.130984

| | | 1.745114

| | | Calculating parameter updates

| | | Iter: 2, Total mss = 8.663118

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 0.639317

| | | 0.430923

| | | 7.204518

| | | 3.347986

| | | 3.017625

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 0.944308

| | | 0.437084

| | | 6.671525

| | | 3.616116

| | | 3.346157

| | | Calculating parameter updates

| | | Iter: 3, Total mss = 8.349780

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 0.979263

| | | 0.431915

| | | 8.247894

| | | 3.701194

| | | 3.383710

| | | Loading prediction maker

| | | Evaluating prediction maker model

| | | Estimated hyperparameters: 0.114984

| | | 0.419787

| | | 7.361230

| | | 2.821078

| | | 2.498557

| | | Calculating parameter updates

| | | Iter: 4, Total mss = 8.179681

| | | 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: 0.449439

| | | 0.443579

| | | 7.145599

| | | 0.901422

| | | 0.572428

| | | Running sm.WriteParameterFile

| | | Running sm.WriteRegisteredImages

| | | Running sm.RecycleOutliers

| | | Running sm.WriteRotatedBVecs

| | | Running sm.WriteMovementRMS

| | | completed.

| | |_12.5562 m

| | update b-table from eddy output

| | load topup/eddy results

| | found bval and bvec file for /Volumes/T7/ABCDTI2/ABC1023/ABC/DTI_20191211130957_12_dwi_AP.nii.src.gz.corrected.nii.gz

| | generating mask

| |_13.4128 m

|_13.4128 m

process SRC files

| processing /Volumes/T7/ABCDTI2/ABC1023/ABC/DTI_20191211130957_12_dwi_AP.nii.src.gz

|-initializing

| | 11ReadDWIData

| | 13BalanceScheme

| | 9GQI_Recon

| | 8RecordQA

| |_7 ms

|-Preparing QA/ISO maps for normalization

| |_3.59 s

|-initializing

| | 16DWINormalization

| |-QA/ISO normalization

| | | ratio lower than 0.5, downsampling template to 2 mm resolution

| | |-linear registration

| | | | [thread]translocation: -2.11388 0.107336 5.40986

| | | | [thread]rotation: 0.00738088 0.0162175 0.0207777

| | | | [thread]scaling: 0.885472 1.00203 0.922487

| | | | [thread]shear: 0.029916 -0.0154759 0.00174498

| | | |_42.537 s

| | | linear R2: 0.488535

| | |-normalization

| | | |_9.664 s

| | | linear+nonlinear R2: 0.770116

| | | output resolution: 2.2

| | | output dimension: (70,85,61)

| | |_52.29 s

| | 10Dwi2Tensor

| | 13BalanceScheme

| | 9GQI_Recon

| | 9RDI_Recon

| | 11SaveMetrics

| |_52.293 s

|-QSDR reconstruction

| |_31.651 s

|-output

| | 16DWINormalization

| | 10Dwi2Tensor

| | 13BalanceScheme

| | 9GQI_Recon

| | 9RDI_Recon

| | 11SaveMetrics

| |_428 ms

| FIB file saved: /Volumes/T7/ABCDTI2/ABC1023/ABC/DTI_20191211130957_12_dwi_AP.nii.src.gz.icbm152_adult.qsdr.1.25.R77.fib.gz

| generating mask

|_1.53785 m

open FIB file DTI_20191211130957_12_dwi_AP.nii.src.gz.icbm152_adult.qsdr.1.25.R77.fib.gz

I'll also check the GUI to batch process all data in the meantime. Thank you!

Best,

Ida

Frank Yeh

unread,

Mar 18, 2024, 11:39:54 AMMar 18

to rangu...@gmail.com, DSI Studio

The output suggests the cause:

The CLI is calling the FSL TOPUP installed at
/Users/idarangus/fsl/bin/topup and it crashed.

The GUI is calling the TinyFSL's TOPUP at
/Applications/dsi_studio.app/Contents/MacOS/plugin/topup

| | | run /Applications/dsi_studio.app/Contents/MacOS/plugin/topup

A quick solution is to remove FSL topup/eddy installation at
/Users/idarangus/fsl/bin/ and see if DSI Studio uses the TinyFSL
included in the dsi_studio app package .

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/a984de45-0274-4579-9bcb-f1502ce433d8n%40googlegroups.com.

Ida R.

unread,

Mar 20, 2024, 5:46:45 PMMar 20

to DSI Studio

Thanks a lot, this makes sense. I removed the topup and eddy installations from the FSL bin and now the tinyFSL within the DSI Studio is being recognized and used, but the topup still crashes (unknown error), any idea what could be causing this and if there is some other solution? I tried the batch processing with the GUI, but I don't think it recognizes different reverse pe images per participant, so I'd prefer to work with the script.

| | | [1;31mERROR: Unknown error [0m

[1;34mDSI Studio version: Chen"陳" Feb 5 2024 [0m
| [0;33mDSI Studio version [0m: Chen"陳"
| [0;32maction [0m=rec

| [0;32msource [0m=/Volumes/T7/ABCDTI2/ABC1022/ABC/DTI_20191210130809_12_dwi_AP.nii.src.gz
| [0;32mloop [0m=/Volumes/T7/ABCDTI2/ABC1022/ABC/DTI_20191210130809_12_dwi_AP.nii.src.gz

|- [1;34mrun rec [0m

| | | [0;32mrev_pe [0m=/Volumes/T7/ABCDTI2/ABC1022/ABC/DTIrev_20191210130809_14_dwi_rev.nii

| | | | | [0;33mprojected correction [0m: 0.924619 0.998301 0
| | | | | [0;33msource com [0m: 50.0556 53.2222 38.6667
| | | | | [0;33mrev pe com [0m: 50.4286 25.254 9.63492

| | | | | [0;33msource and reverse phase encoding [0m: AP_PA

| | | | | create acq params at DTI_20191210130809_12_dwi_AP.topup.acqparams.txt

| | | | | [0;33mpath [0m: /Volumes/T7/ABCDTI2/ABC1022/ABC
| | | | | [0;32m--imain [0m=DTI_20191210130809_12_dwi_AP.topup.AP_PA.nii.gz
| | | | | [0;32m--datain [0m=DTI_20191210130809_12_dwi_AP.topup.acqparams.txt
| | | | | [0;32m--out [0m=DTI_20191210130809_12_dwi_AP
| | | | | [0;32m--iout [0m=DTI_20191210130809_12_dwi_AP.topup.check_result

| | | | |_307 ms
| | | |_307 ms

| | | [1;31mERROR: Unknown error [0m

| | |_308 ms
| |_771 ms
|_775 ms

[1;31mWARNING: --save_src is not used/recognized. [0m

Best,

Ida

Frank Yeh

unread,

Mar 21, 2024, 3:53:26 PMMar 21

to rangu...@gmail.com, DSI Studio

So if I understand correctly, some SRC files could be processed
successfully by GUI, and some did not?

If that is the case, perhaps it is the issue with the data, and you
may check out if there are any differences in the data acquisition.

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/fd50d24e-2fb4-49a5-afe8-80563488f548n%40googlegroups.com.

Message has been deleted

Frank Yeh

unread,

Mar 22, 2024, 3:11:27 PMMar 22

to rangu...@gmail.com, DSI Studio

You may change how you name the PA images so that it works for all SRC files.
DSI Studio's console will tell what exactly it is looking for the 2nd
SRC file, and you may rename it accordingly.

Hope this helps,
Frank

On Fri, Mar 22, 2024 at 3:04 PM Ida R. <rangu...@gmail.com> wrote:
>
> The problem I encounter with GUI when trying to perform topup/eddy correction using batch processing Step B3 (SRC to FIB) is that I can specify a directory containing all the src files (AP images), but when I try to specify the PA images for the topup/eddy correction steps, I can only specify one file (and not the whole directory with the PA dwi images needed for separate correction per participant), that's why I believe it stops after the first participant, which makes sense. I can't find the option to specify the whole directory with PA images.
>
> Best,
> Ida

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/1fe34ff1-857d-4f29-b983-81ffa1860d7bn%40googlegroups.com.

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