No MNI to T1w Transform - Multiple sessions


I am encountering an issue with the qsiprep reconstruction step. I am trying to run reconstruction for a single subject, which includes multiple sessions. While the first session will run successfully, the following sessions fail to process. I also compared the two sessions anat directory files and was not able to see any differences between them. Despite this, I will get the following error when the processing gets to the second session:

Exception: No MNI to T1w transform found in anatomical directory

Any help or suggestions would greatly be appreciated.

Thank you so much!


singularity run --cleanenv \
-B /autofs -B /usr/pubsw \
-B /cluster -B /homes -B /space -B /vast -B /run/user \
        $qsiprep \
        $BIDS_DIR $Derivatives_DIR participant \
    --participant_label ${SUBJECTS} \
    --recon-input $QSIPrep_DIR \
    --recon-spec dsi_studio_gqi \
    --output-resolution 1.3  \
    --work-dir ${Work_DIR}  \
    --fs-license-file ${fsLicense} \
    --mem_mb 30000


qsiprep version 0.19.0

Relevant log outputs:

crash.txt (1.9 KB)

Hi @onewman and welcome to neurostars!

Does this error persist with the most recent version 0.20.0?


Our lab seems to be experiencing the same issue. (recon is failing for the second session in longitudinal runs). We are seeing this across multiple datasets, and across multiple recon workflows.

Also, has version 0.20.0 been released? I only see 0.19.0 mentioned in the documentation.