Where is the output?

[jcohenadad]

Commit: 71012eb588933e0a2fe55a6078927e5a91d7a92e

I launched a nextflow, but I don't know where the output is supposed to be located. Nothing that seems like output processed files was created on my local folder. This info should be added in the README.

Terminal output

``` julien-macbook:~/code/anat-processing $ nextflow run neuromod-process-anat.nf --bids ~/data/neuromod/ N E X T F L O W ~ version 20.10.0 Launching `neuromod-process-anat.nf` [boring_swanson] - revision: 0f8d97f33c WARN: There's no process matching config selector: mtsat_align_inputs WARN: There's no process matching config selector: publish_outputs WARN: There's no process matching config selector: extract_brain -- Did you mean: Extract_Brain? Using Octave in Docker or (if local) from the sys path. Input: /Users/julien/data/neuromod/ qMRflow: MTsat pipeline ======================= ## ## ######## ###### ### ######## ### ### ## ## ## ## ## ## #### #### ## ## ## ## ## ## ### ## ## ###### ## ## ## ## ## ## ## ######### ## ## ## ## ## ## ## ## ## ## ## ## ###### ## ## ## Start time: 2021-04-06T10:13:44.718062-04:00 DATA ==== BIDS option has been enabled. WARN: qMRI protocols will be read from sidecar .json files. OPTIONS ======= [GLOBAL] --------------- Selected platform: octave BET enabled: true B1+ correction enabled: true [ANTs Registration] ------------------- Dimensionality: 3 Metric: MI Weight: 1 Number of bins: 32 Sampling type: Regular Sampling percentage: 0.25 Transform: Rigid[0.1] Convergence: [1000x500x250x100,1e-6,10] Shrink factors: 8x4x2x1 Smoothing sigmas: 3x2x1x0vox [FSL BET] --------------- Enabled: true Fractional intensity threshold: 0.45 Robust brain center estimation: true [qMRLab mt_sat] --------------- WARN: Acquisition protocols will be read from sidecar .json files (BIDS). B1+ correction has been ENABLED. WARN: Process will be skipped for participants missing a B1map file. B1 correction factor: 0.4 ======================= [- ] process > Align_Input_Volumes - [- ] process > Extract_Brain - [- ] process > B1_Align - [- ] process > B1_Smooth_With_Mask - [- ] process > B1_Smooth_Without_Mask - [- ] process > Fit_MTsat_With_B1map_With_Bet - [- ] process > Fit_MTsat_With_B1map_Without_Bet - [- ] process > Fit_MTsat_Without_B1map_With_Bet - [- ] process > Fit_MTsat_Without_B1map_Without_Bet - Pipeline completed at: 2021-04-06T10:13:46.669629-04:00 Execution status: OK Execution duration: 2s julien-macbook:~/code/anat-processing $ ll total 120 drwxr-xr-x 14 julien staff 448 6 Apr 10:13 . drwxr-xr-x 65 julien staff 2080 1 Apr 21:18 .. drwxr-xr-x 15 julien staff 480 6 Apr 09:57 .git -rw-r--r-- 1 julien staff 447 6 Apr 09:57 .gitignore drwxr-xr-x 4 julien staff 128 6 Apr 10:13 .nextflow -rw-r--r-- 1 julien staff 11777 6 Apr 10:13 .nextflow.log -rw-r--r-- 1 julien staff 1074 2 Feb 12:13 LICENSE -rw-r--r-- 1 julien staff 1594 6 Apr 09:57 README.md drwxr-xr-x 4 julien staff 128 6 Apr 09:57 containers drwxr-xr-x 5 julien staff 160 6 Apr 09:57 modules -rw-r--r-- 1 julien staff 21021 6 Apr 09:57 neuromod-process-anat.nf -rw-r--r-- 1 julien staff 7023 6 Apr 09:57 neuromod_anat_dsl2.nf -rw-r--r-- 1 julien staff 2211 6 Apr 09:57 nextflow.config drwxr-xr-x 2 julien staff 64 6 Apr 10:13 work ```

[agahkarakuzu]

Right now the old version cannot capture data channels because of the changes made to the data organization since I first developed that workflow. I will push a small change to that workflow to capture channels for you to test. But eventually, we will have a master change on neuromod-process-anat.nf.

[jcohenadad]

Right now the old version cannot capture data channels because of the changes made to the data organization since I first developed that workflow. I will push a small change to that workflow to capture channels for you to test. But eventually, we will have a master change on neuromod-process-anat.nf.

sounds good-- let me know when ready for another pass

[agahkarakuzu]

@jcohenadad on bids_adapt branch you can try

 nextflow run neuromod-process-anat.nf --bids ~/data/neuromod/ -with-report report.html

I limited it to 4CPUs and 4GB memory per process and reduced the process forks, still can be a bit demanding.

This one will save outputs to sub folders sub-01_ses-001, it is handled more elegantly in the new one.

[agahkarakuzu]

It took 14 minutes to finish alignment and skull stripping for 20 datasets. But the process did not move on because the B1maps were not captured.

After my next commit to fix this (unless you delete your work folder (gitignored)), passing -resume argument to the nextflow call would pick up from here.

[jcohenadad]

@jcohenadad on bids_adapt branch you can try

can you pls open a PR so i can comment directly on the PR? thx

[agahkarakuzu]

10