Heudiconv error with latest version heudiconv_1.1.0.sif: WARNING: Could not check for version updates: Connection to server could not be made

Software Support
1

Summary of what happened:

Hi everyone,

I am trying to re-run new subjects for a new site, and am trying to run heudiconv to generate the .tsv file. I keep getting the following error. @yarikoptic Tagging you because it says you are the creator of the 1.1.0.sif latest version that I pulled. Thank you.

Command used (and if a helper script was used, a link to the helper script or the command generated):

#!/bin/bash
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --account=PAS2302

project=$1
subject=$2

echo "Running heudiconv initial script"

singularity run --cleanenv \
/fs/ess/PAS2302/Subbi/TURBO/TERBO/heudiconv_1.1.0.sif \
-d /fs/ess/PCON0340/SOAR_Temp/MRI/RAW_DATA/$project/arc001/{subject}_??-??/SCANS/*/DICOM/* \
-o /fs/ess/PCON0340/SOAR_Temp/MRI/$project/NIFTI \
-f convertall \
-s $subject \
-c none ;

echo "Finished subject" $subject

Version:

1.1.0

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

WARNING: Could not check for version updates: Connection to server could not be made
INFO: Running heudiconv version 1.0.1 latest Unknown
INFO: Need to process 0 study sessions
Finished subject 70001-01_01-23

Screenshots / relevant information:

I ran it with the --cleanenv and the --no-home flag but get the same error for both. Is anyone else running into this issue?

Above for some reason says 1.0.1 even through its path is to the 1.1.0 sif file.

2

(edit: post was merged with original post above)

3

you seems never bound mount that folder inside container . Add -B /fs/ess/PCON0340/SOAR_Temp/MRI/ right after run ?

4

Hello, I’m currently running my previous script which worked properly, and I’m getting the same error:

WARNING: Could not check for version updates: Connection to server could not be made
INFO: Running heudiconv version 1.0.1 latest Unknown
INFO: Need to process 0 study sessions

Im working in docker by Neurodesk.
Do you have any suggestion about how to solve it?
Thanks in advance.
Patricio

5

Hi,

I mounted it to the base and am still getting the same error:

Singularity Script:

Singularity
Singularity803×570 42.9 KB

Error:

Singularity Error
Singularity Error928×226 18.5 KB

CLI:
sbatch osc_heudiconv_initial_SOAR_SM.sh SOAR_Mobile 70001-01_01-23 01

6

I may be missing something. What is the error? I see a warning, but is there something actually failing?

7

Hi,

That is the error. It does not create the hidden directory in the heudiconv folder. Nothing is being generated. I originally thought that it was an issue with the path to my dicom files but when I ran the script last week it worked. It simply crashes with the above error without generating anything.

Thanks.

–Subbi M.

8

Hi @Steven could you close this?

It has been resolved on my end. Figured out the problem.

Thanks.

–Subbi M.