No MNI to T1w transform - QSIrecon

Hi,

I am encountering the attached error from qsirecon. I am running into this on some subjects while for others, I am able to successfully run reconstruction. I compared the anat directory from two subjects (that ran successfully and unsuccessfully) from qsiprep (input to recon) and am not able to discern differences in the files within them.

Can anyone advise on what is happening?

Thanks in advance.

Hi,

What was the command you used to run QSIPrep? And for QSIRecon? Did you run the anatomical workflow during preprocessing (that is, no --dwi-only flag)? What version of QSIPrep?

Best,
Steven

Hi,

I am using 0.16.1 version of qsiprep.

The qsiprep command I used to run preprocessing is as follows:

singularity run --cleanenv -B /mnt/cina/WMH:/WMH ${qsiprep_img) ${BIDS_dir} ${output_dir} participant -w ${work_dir}--participant-label ${subj} --output-resolution 1.0 --fs_license_file ${FS_LICENSE} --skips -validation--nthreads 16 --mem-mb 16000

The qsirecon command I used for reconstruction is as follows:

singularity run --cleanenv -B /mnt/cina/WMH:/WMH /mnt/cina/WMH/lib/qsiprep-0.16.1.simg /WMH/data/BIDS/ADNI/ /WMH/data/BIDS/ADNI/derivatives/qsiprep participant --participant_label sub-036S6179--output-resolution 1.0 --recon-only --recon-spec amico_noddi --recon-spec dsi_studio_gqi --recon-input /WMH/data/BIDS/ADNI/derivatives/qsiprep/qsiprep --fs_license_file /WMH/lib/fs_license.txt --skip-bids-validation

Thanks in advance.

For your QSIRecon command, I would set the output dir and recon-input as /WMH/data/BIDS/ADNI/derivatives/, unless the qsiprep outputs are in a folder called derivatives/qsiprep/qsiprep

Also, lets try only having one recon-spec. You can combine the amico_noddi and dsi_studio_gqi workflows into one recon_spec by combining their jsons, like so:

{ "description": "Runs the AMICO implementation of NODDI",
  "space": "T1w",
  "name": "amico_noddi",
  "atlases": ["schaefer100", "schaefer200", "schaefer400", "brainnetome246", "aicha384", "gordon333", "aal116"],
  "nodes": [
    {
      "name": "fit_noddi",
      "action": "fit_noddi",
      "software": "AMICO",
      "input": "qsiprep",
      "output_suffix": "NODDI",
      "parameters": {
        "isExvivo": false,
        "dPar": 1.7E-3,
        "dIso": 3.0E-3
      }
    {
      "name": "dsistudio_gqi",
      "software": "DSI Studio",
      "action": "reconstruction",
      "input": "qsiprep",
      "output_suffix": "gqi",
      "parameters": {"method": "gqi"}
    },
    {
      "name": "scalar_export",
      "software": "DSI Studio",
      "action": "export",
      "input": "dsistudio_gqi",
      "output_suffix": "gqiscalar"
    },
    {
      "name": "tractography",
      "software": "DSI Studio",
      "action": "tractography",
      "input": "dsistudio_gqi",
      "parameters": {
        "turning_angle": 35,
        "method": 0,
        "smoothing": 0.0,
        "step_size": 1.0,
        "min_length": 30,
        "max_length": 250,
        "seed_plan": 0,
        "interpolation": 0,
        "initial_dir": 2,
        "fiber_count": 5000000
      }
    },
    {
      "name": "streamline_connectivity",
      "software": "DSI Studio",
      "action": "connectivity",
      "input": "tractography",
      "output_suffix": "gqinetwork",
      "parameters": {
        "connectivity_value": "count,ncount,mean_length,gfa",
        "connectivity_type": "pass,end"
      }
    }
  ]
}

You can save that as a .json file, and put the path to that as your --recon-spec, and make sure it is contained in a path that is bound to the container (somewhere in /mnt/cina/WMH/).

So, after checking to make sure QSIPrep ran successfully for these subjects (e.g., checking the HTML outputs, I would run this command for QSIRecon, using a fresh work directory:

singularity run --cleanenv -B /mnt/cina/WMH:/WMH /mnt/cina/WMH/lib/qsiprep-0.16.1.simg /WMH/data/BIDS/ADNI/ /WMH/data/BIDS/ADNI/derivatives/ participant --participant_label sub-036S6179 --recon-only --recon-spec /PATH/TO/YOUR/RECON/SPEC.json --recon-input /WMH/data/BIDS/ADNI/derivatives/qsiprep/ --fs_license_file /WMH/lib/fs_license.txt --skip-bids-validation -w SPECIFY/WORK/DIR