Amico_NODDI reconstruction does not return any Results

Software Support
,
1

Summary of what happened:

I used the following command for QSIPrep and used --recon-spec amico_noddi. It ran fine and generate the preprocessing files fine. However I cannot see any Amico NODDI results. Am I miisng something.

Command used

singularity run --containall --writable-tmpfs -B /home/Amubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/,/home/Amubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/Results,/mnt/space,${FREESURFER_HOME}/license.txt:/opt/freesurfer/freesurfer/license.txt qsiprep-0.22.0.sif /home/Amubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/ /home/Amubeen/onrc/data/NODDI/qsiprep/AP_17mmMB4/Results -w /mnt/space --output-resolution 1.2 participant --participant_label sub-S00001 sub-S00002 --recon-spec amico_noddi --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?

BIDS Standard

2

Hi @asim.mubeen,

It would help to see the log of the run and tree directory structure on the qsirecon output folder.

Best,
Steven

3

Hi Steven,

Thanks for your reply. It did not create qsirecon folder. And where can I find the log of the run? (I am sorry, I am new to QSIPrep).

Best,

–
Asim

4

Hi @asim.mubeen,

If running directly in the terminal, it would be the terminal output. Otherwise, if using a job scheduler (like SLURM or SGE), it would be the standard .out log that should be created in whatever directory you submitted the jobs from.

Best,
Steven

5

Steven,

A text file is attached that has the log for the run.
Log.txt (655.0 KB)

–
Asim

6

Hi @asim.mubeen,

Can you try rerunning and adding the --recon-only and --recon-input flag (the second flag should point to the qsiprep output folder)?

Best,
Steven

1 Like
7

Steven,

Thank you very much. It works!!! Now I have a few questions:

  1. Do I need to run the qsiprep first and then run the reconstruction the way you explained?
  2. With qsirecon available, is it better to run qsiprep first and then run reconstruction via qsirecon?
  3. Is there any difference among the above two approaches? OR they are the same workflow ?

Best.

–
Asim

8

Hi @asim.mubeen,

In theory, no. It is supposed to go straight into it. However, there were some (non-fatal) errors in the log, and perhaps that precluded the qsiprep-to-qsirecon transition.

Beginning in version 0.23.0, yes this is how to do it moving forward.

It’s the same in principle. Of course there were be differences between software versions.

Best,
Steven

1 Like