QSIPrep Space Error

Software Support
1

Summary of what happened:

Hi Neurostars!

I am new to QSIPrep, and trying to run it via singularity. I checked there is enough space. I am not sure what is going wrong!

Asim

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

singularity run \
--containall \
--writable-tmpfs \
-B /home/mubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/,/home/mubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/Results,${FREESURFER_HOME}/license.txt:/opt/freesurfer/freesurfer/license.txt \
qsiprep-0.22.0.sif \
/home/mubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/ \
/home/mubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/Results \
-w /tmp \
--output-resolution 2 \
participant \
--participant_label sub-S0001009 \
--fs-license-file /opt/freesurfer/freesurfer/license.txt

Version:

0.22.0

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):


FileNotFoundError: /tmp/qsiprep_0_22_wf/sub_S0001009_wf/anat_preproc_wf/anat_template_wf/template_dimensions/result_template_dimensions.pklz

The above is the last error in a list of similar errors.
The first error was:

 nipype.workflow WARNING:
         Storing result file without outputs
240909-20:33:48,427 nipype.workflow WARNING:
         [Node] Error on "qsiprep_0_22_wf.sub_S0001009_wf.dwi_preproc_ses_0001_wf.pre_hmc_wf.merge_and_denoise_wf.conform_dwis01" (/tmp/qsiprep_0_22_wf/sub_S0001009_wf/dwi_preproc_ses_0001_wf/pre_hmc_wf/merge_and_denoise_wf/conform_dwis01)

Screenshots / relevant information:

2

Hi @asim.mubeen,

In the future, please use the Software Support category which prompts you for important information and helps organize your post. You can see I reorganized your post for you this time.

Please return the full error traceback (even the full log attached as a .txt would help). I think there is more there that would help us debug. The BIDS validation report may also help. I also noticed you did not bind a local drive to /tmp, perhaps doing so would help.

Best,
Steven

1 Like
3

Steven,

Thank you very much for the prompt reply. Binding /tmp helps and I may get back if I have any other questions. And for future I’ll use “Software Support”.

Thanks again!

–
Asim

1 Like