How do I run with a session?

[dkp]

Hi Robert,

I am using the version of MRtrix3_connectome from Dockerhub, having converted it to a Singularity container. I am running on our HPC. I guess I have never tried to run it on a participant directory with a nested session (it is also under Datalad control).

I get back complaints that it cannot find the dwi or fmap directories:

mrtrix3_connectome.py:
mrtrix3_connectome.py: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
mrtrix3_connectome.py:
Command: bids-validator /bids_dataset
mrtrix3_connectome.py: Commencing execution for subject sub-219
mrtrix3_connectome.py: N4BiasFieldCorrection and ROBEX found; will use for bias field correction and brain extraction
mrtrix3_connectome.py: Generated temporary directory: /home/u7/dkp/mrtrix3_connectome.py-tmp-BT1W22/
mrtrix3_connectome.py: Importing DWI data into temporary directory
mrtrix3_connectome.py: [ERROR] Inadequate data for pre-processing of subject 'sub-219': No phase-encoding contrast in input DWIs, and no fmap/ directory, so EPI distortion correction cannot be performed
mrtrix3_connectome.py: Contents of temporary directory kept, location: /home/u7/dkp/mrtrix3_connectome.py-tmp-BT1W22/
Your group dkp has been charged 0:01:20 (0:00:05 X 16 cpus).
You previously had 7000:00:00. You now have 6999:58:40 of el_standard_time remaining

========================

Here is what the directory structure looks like:

sub-219/ses-itbs:
anat
dwi
fmap
func
sub-219_ses-itbs_scans.json
sub-219_ses-itbs_scans.tsv

sub-219/ses-itbs/anat:
sub-219_ses-itbs_T1w.json
sub-219_ses-itbs_T1w.nii.gz
sub-219_ses-itbs_acq-tse_T2w1.json
sub-219_ses-itbs_acq-tse_T2w1.nii.gz
sub-219_ses-itbs_acq-tse_T2w2.json
sub-219_ses-itbs_acq-tse_T2w2.nii.gz

sub-219/ses-itbs/dwi:
sub-219_ses-itbs_acq-AP_dwi.bval
sub-219_ses-itbs_acq-AP_dwi.bvec
sub-219_ses-itbs_acq-AP_dwi.json
sub-219_ses-itbs_acq-AP_dwi.nii.gz

sub-219/ses-itbs/fmap:
sub-219_ses-itbs_dir-PA_epi.json
sub-219_ses-itbs_dir-PA_epi.nii.gz
sub-219_ses-itbs_magnitude1.json
sub-219_ses-itbs_magnitude1.nii.gz
sub-219_ses-itbs_magnitude2.json
sub-219_ses-itbs_magnitude2.nii.gz
sub-219_ses-itbs_phasediff.json
sub-219_ses-itbs_phasediff.nii.gz

sub-219/ses-itbs/func:
sub-219_ses-itbs_acq-asl_run-01.json
sub-219_ses-itbs_acq-asl_run-01.nii.gz
sub-219_ses-itbs_acq-asl_run-02.json
sub-219_ses-itbs_acq-asl_run-02.nii.gz
sub-219_ses-itbs_task-rest_run-01_bold.json
sub-219_ses-itbs_task-rest_run-01_bold.nii.gz
sub-219_ses-itbs_task-rest_run-01_events.tsv
sub-219_ses-itbs_task-rest_run-02_bold.json
sub-219_ses-itbs_task-rest_run-02_bold.nii.gz
sub-219_ses-itbs_task-rest_run-02_events.tsv

My script looks like this (no explicit mention of sessions, but I do not see that option in your help):

# Define a variable to point to the directory you want to work in
# This is not strictly necessary, but may be helpful
export STUFF=/groups/dkp/
export MRIS=${STUFF}/Nifti

# Just to be safe, create the mrtrix_hcpmmp1 directory if it does not exist.
if [ ! -d ${MRIS}/derivatives/mrtrix_hcpmmp1 ]; then
mkdir -p ${MRIS}/derivatives/mrtrix_hcpmmp1
fi

module load singularity

Subject=${sub}

singularity run --cleanenv --bind ${MRIS}:/bids_dataset --bind ${MRIS}/derivatives/mrtrix_hcpmmp1:/outputs ${SIF}/mrtrix3_connectome.sif /bids_dataset /outputs participant --participant_label ${Subject} --parcellation hcpmmp1 --output_verbosity 3

=================

Just to make sure I'm not crazy, I'm running my script on a simpler version of the same dataset (no nested session), and it is chugging along.

Thoughts?

Thank you,

Dianne

[Lestropie]

Hi Dianne,

"mrtrix3_connectome.py: Commencing execution for subject sub-219"

This is not running the 0.5.0 code. You can see here in the code that that version refers to a "session" being processed, not a "subject", regardless of whether or not there are multiple sessions for any particular subject.

My script looks like this (no explicit mention of sessions, but I do not see that option in your help):

The 0.5.0 code offers the "--session_label" command-line option, which operates in the same way as the --participant_label option. My guess is that you were looking at the documentation on DockerHub, which appears as though it was not automatically updated with the contents of README.md when I pushed the update, and therefore contained outdated information; I've updated that now.

Rob