Error: Unknown error during corrretion and reconstruction

9 views
Skip to first unread message

xitch

unread,
May 22, 2022, 12:52:53 PMMay 22
to DSI Studio
Hi Dr. Yeh,

When I tried to correct and reconstruct the data with the command line, I got an unknown error. Do you know what's going on? To clarify my problem, I attached my command line and the output below. Thank you so much!

Sincerely,
Xitong

Command line I used:
subjects=(20220329_F019Y_10172 20220406_F019Y_10174 20220405_F024Y_10175 20220414_F022Y_10176 20220513_F020Y_10179)

for sub in ${subjects[@]}
do
input=/Shared/lss_kahwang_hpc/ThalHi_Diffusion/SRC_folder/${sub}_s06_HCPDTI.src.gz

reversed=/Shared/lss_kahwang_hpc/ThalHi_Diffusion/SRC_folder/${sub}_s05_DWIB0.nii.gz

singularity exec /Shared/lss_kahwang_hpc/opt/dsi_studio_latest/dsistudio_latest.sif dsi_studio \
--action=rec --source=${input} --rev_pe=${reversed} --method=7 --param0=1.25 --check_btable=1 \
--output=/Shared/lss_kahwang_hpc/ThalHi_Diffusion/Corrected_folder/
done

The output of one subject. I got the same error for all of them. 
Running on compute node: argon-itf-bx47-40.hpc.
In directory: /Shared/lss_kahwang_hpc/ThalHi_Diffusion
Starting on: Sun May 22 11:47:37 CDT 2022
DSI Studio "Chen" May 15 2022
source=/Shared/lss_kahwang_hpc/ThalHi_Diffusion/SRC_folder/20220329_F019Y_10172_s06_HCPDTI.src.gz
action=rec
loading source...
prepare index file for future accelerated loading
SRC file loaded
src loaded
rev_pe=/Shared/lss_kahwang_hpc/ThalHi_Diffusion/SRC_folder/20220329_F019Y_10172_s05_DWIB0.nii.gz
topup/eddy
projected correction:0.938253 0.983177 0
source com:57.4211 55.5789 23.2632
rev pe com:65.8333 30.6111 16.6111
source and reverse phase encoding: AP_PA
create acq params at 20220329_F019Y_10172_s06_HCPDTI.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
FSL installation found at /opt/fsl
run /opt/fsl/bin/topup at /Shared/lss_kahwang_hpc/ThalHi_Diffusion/SRC_folder with
--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=20220329_F019Y_10172_s06_HCPDTI.topup.AP_PA.nii.gz
--datain=20220329_F019Y_10172_s06_HCPDTI.topup.acqparams.txt
--out=20220329_F019Y_10172_s06_HCPDTI
--iout=20220329_F019Y_10172_s06_HCPDTI.topup.check_result
--verbose=1
ERROR:Unknown error
Warning: --method is not used. Please check command line syntax.
Warning: --param0 is not used. Please check command line syntax.
Warning: --check_btable is not used. Please check command line syntax.
Warning: --output is not used. Please check command line syntax.

Frank Yeh

unread,
May 23, 2022, 8:00:28 AMMay 23
to dsi-s...@googlegroups.com
It seems that FSL eddy reported an error.
Could you send the SRC file and the reversed PE b0 to me?

Frank

xitch

unread,
May 23, 2022, 11:22:50 AMMay 23
to dsi-s...@googlegroups.com
Hi Dr. Yeh,

Thanks for your reply! I attached a dropbox link below. The data is from this batch of subjects. Let me know if you need anything additional from me. Thank you!

https://www.dropbox.com/sh/asfg6b9g423ko2d/AABocw65sH65LJ6rfI7jIoBNa?dl=0

Sincerely,
Xitong
> --
> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtJWUagRsY7knr7a4DdOCPDqXMk4w34qwQpcsjC-6h4tVg%40mail.gmail.com.

Frank Yeh

unread,
May 23, 2022, 11:34:36 AMMay 23
to dsi-s...@googlegroups.com
I downloaded the data and you may remove the link.
There is a private upload link on DSI Studio website ("Data Upload"),
and you may use it in the future.
I will get back to you soon.
Frank
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/FE740D26-AEC2-40F4-94B3-E48BF2052338%40gmail.com.

xitch

unread,
May 23, 2022, 12:03:37 PMMay 23
to dsi-s...@googlegroups.com

Frank Yeh

unread,
May 23, 2022, 12:07:33 PMMay 23
to dsi-s...@googlegroups.com
I can run TOPUP/EDDY on my side.
It seems that in your case, the FSL topup cannot be initiated.

Did you use singularity?
Frank
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/A9AF66FB-EE1B-497A-B010-F6F41713FF98%40gmail.com.

Frank Yeh

unread,
May 23, 2022, 12:10:14 PMMay 23
to dsi-s...@googlegroups.com
You may try updating DSI Studio again and see if it works.
Frank

xitch

unread,
May 23, 2022, 9:49:35 PMMay 23
to dsi-s...@googlegroups.com
Hi Dr. Yeh,

I got it! It just because my current working directory is not as same as the input file. So some output of TOPUP/EDDY were not found. Thank you for your help!

Sincerely,
Xitong

Reply all
Reply to author
Forward
0 new messages