Command Line Issue: Generate src/nifti file from DICOM

[xitch]

Hi Dr. Yeh,

I got an issue when I tried to use --action=src to generate src/nifti from DICOM files. The error is "cannot find b-table from the header. You may need to load an external b-table using--b_table or --bval and --bvec." But I can successfully generate src and nifti files by operating GUI (use [Batch processing][Step B2c: DICOM to SRC] and select the renamed folder from  [Batch processing][Step B1b: Rename DICOM in Subfolders]). Do you know what's going on? Thanks!

Sincerely,

XT

[Frank Yeh]

Could you post the full log output?

Frank

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[xitch]

Thanks for your quick reply! Sure. Here's my full output

Running on compute node: argon-itf-bx47-39.hpc.
In directory: /Shared/lss_kahwang_hpc/ThalHi_Diffusion
Starting on: Sun Jan 2 18:46:00 CST 2022
DSI Studio "Chen" Dec 28 2021
source=/Shared/lss_kahwang_hpc/ThalHi_Diffusion/Processed_Data/20210625_F021Y_10002
action=src
load files in directory /Shared/lss_kahwang_hpc/ThalHi_Diffusion/Processed_Data/20210625_F021Y_10002
search recursively in the subdir
a total of 36675 files found in the directory
reading 3PlaneLocSSFSE_i1.dcm

cannot find b-table from the header. You may need to load an external b-table using--b_table or --bval and --bvec.

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

Please let me know if you need more information. Thanks!

[xitch]

And also my code below:

singularity exec /Shared/lss_kahwang_hpc/opt/dsi_studio_argon/dsistudio_latest.sif dsi_studio --action=src --source=${input} --recursive=1

在2022年1月2日星期日 UTC-6 11:39:22<Frank Yeh> 写道：

[Frank Yeh]

You may need to rename DICOM files first and only include DWI when creating the SRC file. 

http://dsi-studio.labsolver.org/doc/gui_t1.html

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/865f7642-9d79-489d-b634-6ae37333364cn%40googlegroups.com.

[Frank Yeh]

or you may wait until I fix DSI Studio to hadle it. Should be ready in one hour or two.

Frank

[xitch]

I have renamed it with command line (—action=ren). The input of the code above is the renamed folder. I also tried to generate src/nifti file from DICOM with GUI operation(I chose the renamed folder generated by command line). It works. But when I used the command line(—action =src), it didn’t work. 

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtKxp8xSZ%3DtRyYcK951V%3DdWAWoWSEApfaoUzncf1mUE1nQ%40mail.gmail.com.

[Frank Yeh]

I updated DSI Studio. Please see if the updated version works for you.

Frank

[xitch]

I tried the latest version. It didn't give me the same error message. But I didn't see any new file was generated after running it. And the command was terminated pretty fast, unlike GUI. I thought something is wrong?

Below is the output log. Thanks!

DSI Studio "Chen" Jan  3 2022
source=/mnt/nfs/lss/lss_kahwang_hpc/ThalHi_Diffusion/Processed_Data/20210625_F021Y_10002
action=src
load files in directory /mnt/nfs/lss/lss_kahwang_hpc/ThalHi_Diffusion/Processed_Data/20210625_F021Y_10002

search recursively in the subdir

process folder

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

Frank Yeh <fran...@gmail.com> 于2022年1月3日周一 10:03写道：

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[Frank Yeh]

assign --source=/mnt/nfs/lss/lss_kahwang_hpc/ThalHi_Diffusion/Processed_Data/ should solve the problem.

Frank

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CADr0BjgDouPi1hKB7emb8ikf%3DmYm0GftZwiCx4N4OFmd-vVmxw%40mail.gmail.com.

[xitch]

It works! Thank you so much!

XT

Frank Yeh <fran...@gmail.com> 于2022年1月3日周一 15:05写道：

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