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USAGE
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USAGE
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TractoInferno Tracking pipeline
===================
Run TractoInferno Tracking pipeline (Local Det, Local Prob, PFT Prob)
USAGE
nextflow run main.nf [OPTIONAL_ARGUMENTS] (--input)
DESCRIPTION
--input=/path/to/[root] Root folder containing multiple subjects
[root]
├── S1
| ├── DTI_Metrics
| │ └── fa.nii.gz
│ ├── FODF_Metrics
| │ └── fodf.nii.gz
│ ├── PFT_Maps
| │ ├── interface.nii.gz
| │ ├── map_exclude.nii.gz
| │ └── map_include.nii.gz
│ ├── Segment_Tissues
| │ └── mask_wm.nii.gz
│ └── Seeding_Mask
| └── seeding_mask.nii.gz
└── S2
├── Extract_FODF_Shell
│ └── fodf.nii.gz
├── PFT_Maps
│ ├── interface.nii.gz
│ ├── map_exclude.nii.gz
│ └── map_include.nii.gz
├── Segment_Tissues
│ └── mask_wm.nii.gz
└── Seeding_Mask
└── seeding_mask.nii.gz
Files should be compressed Nifti files (.nii.gz)
OPTIONAL ARGUMENTS (current value)
--pft_seeding_mask_type [PFT] seeding mask type [wm, interface, fa] ($pft_seeding_mask_type).
--pft_fa_seeding_mask_theshold [PFT] FA threshold for FA seeding mask ($pft_fa_seeding_mask_theshold).
--pft_algo [PFT] Tracking algorithm [prob, det] ($pft_algo).
--pft_seeding [PFT] Seeding type [npv, nt] ($pft_seeding).
--pft_nbr_seeds [PFT] Number of seeds related to the seeding type param ($pft_nbr_seeds).
--pft_step [PFT] Step size ($pft_step).
--pft_theta [PFT] Maximum angle between 2 steps ($pft_theta).
--pft_min_len [PFT] Minimum length ($pft_min_len).
--pft_max_len [PFT] Maximum length ($pft_max_len).
--pft_compress_streamlines [PFT] Compress streamlines ($pft_compress_streamlines).
--pft_compress_value [PFT] Compression error threshold ($pft_compress_value).
--pft_random_seed [PFT] List of random seed numbers for the random number generator ($pft_random_seed).
Please write them as list separated using commat WITHOUT SPACE e.g. (--pft_random_seed 0,1,2)
--local_seeding_mask_type [LOCAL] seeding mask type [wm, fa] ($local_seeding_mask_type).
--local_fa_seeding_mask_theshold [LOCAL] FA threshold for FA seeding mask ($local_fa_seeding_mask_theshold).
--local_tracking_mask_type [LOCAL] tracking mask type [wm, fa] ($local_tracking_mask_type).
--local_fa_tracking_mask_theshold [LOCAL] FA threshold for FA tracking mask ($local_fa_tracking_mask_theshold).
--local_seeding [LOCAL] Seeding type [npv, nt] ($local_seeding).
--local_nbr_seeds [LOCAL] Number of seeds related to the seeding type param ($local_nbr_seeds).
--local_step [LOCAL] Step size ($local_step).
--local_theta [LOCAL] Maximum angle between 2 steps ($local_theta).
--local_min_len [LOCAL] Minimum length ($local_min_len).
--local_max_len [LOCAL] Maximum length ($local_max_len).
--local_compress_streamlines [LOCAL] Compress streamlines ($local_compress_streamlines).
--local_compress_value [LOCAL] Compression error threshold ($local_compress_value).
--local_det_random_seed [LOCAL] List of random seed numbers for the random number generator ($local_det_random_seed).
Please write them as list separated using commat WITHOUT SPACE e.g. (--local_det_random_seed 0,1,2)
--local_prob_random_seed [LOCAL] List of random seed numbers for the random number generator ($local_prob_random_seed).
Please write them as list separated using commat WITHOUT SPACE e.g. (--local_prob_random_seed 0,1,2)
--output_dir Directory where to write the final results.
By default, will be in "./results"
--processes The number of parallel processes to launch ($cpu_count).
Only affects the local scheduler.
AVAILABLE PROFILES (using -profile option (e.g. -profile use_cuda,fully_reproducible))
macos When this profile is used, TractoFlow will modify a parameter (scratch) for MacOS users.
NOTES
The 'scilpy/scripts' folder should be in your PATH environment variable. Not necessary if the
Singularity container is used.
The intermediate working directory is, by default, set to './work'.
To change it, use the '-w WORK_DIR' argument.
The default config file is tractoflow/nextflow.config.
Use '-C config_file.config' to specify a non-default configuration file.
The '-C config_file.config' must be inserted after the nextflow call
like 'nextflow -C config_file.config run ...'.