NITRC PANDA: a pipeline tool for diffusion MRI Forum: open-discussion

RE: Job Failure at : Split_WMLabel/Split_WMProbtract

shixin ye — Wed, 17 May 2023 15:54:43 GMT

I successfully solved this problem by using ubuntu16.04, fsl 5.0.9, panda1.3.1. Perhaps you can give it a try

RE: Job Failure at : Split_WMLabel/Split_WMProbtract

shixin ye — Wed, 17 May 2023 15:52:40 GMT

HI，I meet the same problem as yours，I guess it's due to ubuntu using a non English language setting. I successfully processed my data by using ubuntu16.04, fsl 5.0.9, panda1.3.1. Perhaps you can give it a try.

RE: Job Failure at : Split_WMLabel/Split_WMProbtract

yiyao liu — Mon, 06 Mar 2023 13:52:31 GMT

Hello, have you solved the problem of Split -WBLabel failure? I have the same problem as you. If you have solved this problem, could you please tell me the method? Any answer from you is very important to me. I am looking forward to your reply. Thank you

Job Failure at : Split_WMLabel/Split_WMProbtract

Devin Schoen — Fri, 13 Jan 2023 14:04:49 GMT

Hi There,

Has anyone run into a constant job failure at the Split_WBLabel step?

The error message is:

[color=#666699]Something went bad ... the job has FAILED ![/color]
[color=#666699]The last error message occured was :[/color]
[color=#666699]Error using fseek[/color]
[color=#666699]Invalid file identifier. Use fopen to generate a valid file identifier.[/color]
[color=#666699]File /home/devin/Downloads/PANDA_1.3.1_64/g_Split_ROI.m at line 61[/color]
[color=#666699]File /home/devin/Downloads/PANDA_1.3.1_64/psom-1.0.4/psom_run_job.m at line 252[/color]
[color=#666699]File /home/devin/Downloads/PANDA_1.3.1_64/psom-1.0.4/psom_run_job.m at line 166[/color]

[color=#33cccc][color=#666699]To me it seems like there must be a problem with the existence of a file that is called, but I am having a hard time figuring out how to fix it. Any help is appreciated, thanks![/color][/color]

Files Not Importing - "Illegal"

Devin Schoen — Tue, 10 Jan 2023 23:41:49 GMT

[color=#999999]Hi Everyone,[/color]

[color=#999999]I am very new to PANDA and have immediately run into a problem when trying to import a nifti fill using the Full Pipeline functionality.[/color]
[color=#999999]I get the error pop-up: "The input for the 1 subject is illegal".[/color]

[color=#999999]I saw someone make a forum post about this in the past but there didn't didn't seem to be a good explanation/solution.[/color]
[color=#999999]I am wondering if I am just not trying to import the correct information.[/color]

[color=#999999]OS: Linux (Ubuntu 22.04)[/color]
[color=#999999]Panda version: 1.3.1[/color]

[color=#999999]I am just trying to import a single dwi MR .nii file. I also tried to import it in its .nii.gz form. It's alone in the directory I'm trying to pull from. I have tried moving it around to different directories and trying to do everything on an external server. I always get the same error. Do I need to be importing something different? Is there any sort of documentation/tutorial on the import process? I haven't been able to find anything.[/color][list][*][color=#999999]I run the PANDA.m script in matlab[/color][*][color=#999999]I click on the "DICOM/NIFTI Path" button[/color][*][color=#999999]I navigate to the folder and then click on the directory containing my nifti file, it gets added to the bottom box and says "Selected 1 directory."[/color][*][color=#999999]I click "Done" and then I get the illegal message[/color][/list][color=#999999]Should I be doing something differently? [/color]

[color=#000000]UPDATE: I found a manual that has the data preparation insturctions! So Hopefully I am fine now.[/color]

Solution: failed job: bedpostX_postproc

Weiyan Wang — Wed, 07 Dec 2022 2:46:45 GMT

When I use the bedpostx command in fsl to process, an error is still reported, but the following information is prompted in the log file:
/usr/bin/env: "python": no such file or directory

Therefore, the solution is to use the following command to install python:
sudo apt-get install python

If there is a "python" file in /usr/bin/, execute the following command instead:
sudo apt-get --reinstall install python-minimal

How to get the source code of Panda

Yishi Wang — Sun, 04 Sep 2022 4:34:56 GMT

Hi,

I'm trying to use the instructions to get the source code of Panda, but I don't know what modules are in the repo and it seems that the repo is empty. Is the source code still available to the public?

Best Regards,
Yishi

Stopped in the state of job name "delete_tmp_file"

zzzbiubiubiu — Thu, 07 Jul 2022 13:02:17 GMT

Hi，
I have encountered a situation where data processing is stuck with job name "delete_tmp_file"，and the 'unfinished steps' is stopped at 105. I don't know how to solve it. Hope someone can answer. Thank you!

cannot start the PANDA

wenjian zheng — Sat, 23 Apr 2022 16:18:16 GMT

Hi,

I have add the PANDA folder in the "Set path", but it didn't work when I type the "PANDA" (undefined function or variable).
Could you help me?
Thank you!

zheng

EDDYCURRENT failed on PANDA

XING GAN — Tue, 30 Mar 2021 1:13:25 GMT

Hi Developers,

I am using PANDA to preprocess DTIs with the main objective of creating networks. and i run my data on ubuntu 20.04 and Matlab R2017a and PANDA_1.3.0. However, I am running to an issue where the EDDYCURRENT stage is failing for all subjects with the same error message:
***************************************************************************
JobName: EDDYCURRENT_00001
Status: failed
***************************************************************************
******************************
Log of the (matlab) job : EDDYCURRENT_00001
Started on 29-Mar-2021 15:19:15
User: ganxing
host : ganxing-virtual-machine
system : unix
******************************
The job starts now !
********************
********************
Something went bad ... the job has FAILED !
The last error message occured was :
ç´¢å¼è¶åºçéµç»´åº¦ã
File /software/PANDA_1.3.1_64/g_EDDYCURRENT.m at line 129
File /software/PANDA_1.3.1_64/psom-1.0.4/psom_run_job.m at line 252
File /software/PANDA_1.3.1_64/psom-1.0.4/psom_run_job.m at line 166
****************
Checking outputs
****************
The output file or directory /home/ganxing/smbshare/test_dti/result/00001/tmp/00001_DWI_01_resample_0000_crop_eddy.nii.gz was successfully generated!
The output file or directory /home/ganxing/smbshare/test_dti/result/00001/native_space/ecclog.mat was successfully generated!
The output file or directory /home/ganxing/smbshare/test_dti/result/00001/tmp/OutputDone/EDDYCURRENT_00001.done has not been generated!
The output file or directory /home/ganxing/smbshare/test_dti/result/00001/tmp/EDDYCURRENT_output.mat has not been generated!
************************************************
29-Mar-2021 15:23:01 : The job has FAILED
Total time used to process the job : 225.10 sec.
************************************************
ans =
logical
1

Thank you for your help.

Best Wishes,
XING GAN