Add tans and provisional code for pfm

contarg/cli/cli.py

@@ -1,8 +1,11 @@
 import click
 from .run_hierarchical import contarg
 from .run_seedmap import contarg as contargsm
+from .run_tans import contarg as contargtans
+from .run_pfm import contarg as contargpfm
 
-contarg = click.CommandCollection(sources=[contarg, contargsm])
+
+contarg = click.CommandCollection(sources=[contarg, contargsm, contargtans, contargpfm])
 
 if __name__ == "__main__":
     contarg()

contarg/cli/run_pfm.py

@@ -0,0 +1,294 @@
+import click
+import os
+import shutil
+from pathlib import Path
+import numpy as np
+import pandas as pd
+import nilearn as nl
+from nilearn import image
+from niworkflows.interfaces.fixes import (
+    FixHeaderApplyTransforms as ApplyTransforms,
+)
+from fmriprep.workflows.bold.resampling import init_bold_surf_wf, init_bold_grayords_wf
+from contarg.utils import (
+    parse_bidsname,
+    build_bidsname,
+    update_bidspath,
+    find_bids_files,
+)
+from contarg.tans import tans_inputs_from_fmriprep
+from contarg.pfm import (
+    build_pfm_inputdir,
+    write_pfm_script,
+    pfm_inputs_from_tedana,
+    pfm_inputs_from_fmriprep,
+)
+import subprocess
+from pkg_resources import resource_filename
+import configparser
+
+
+@click.group()
+def contarg():
+    pass
+
+
+@contarg.group()
+def pfm():
+    pass
+
+
+@pfm.command()
+@click.option(
+    "--fmriprep-dir",
+    type=click.Path(exists=True),
+    help="Path to fmriprep outputs",
+    required=True,
+)
+@click.option("--out-dir", type=click.Path(), help="Path for outputs.", required=True)
+@click.option(
+    "--tedana-dir",
+    type=click.Path(),
+    default=None,
+    help="Path to TEDANA outputs",
+)
+@click.option(
+    "--subjects-dir",
+    type=click.Path(exists=True),
+    default=None,
+    help="Path freesurfer directory, defaults to {fmriprep_dir}/sourcedata/freesurfer. "
+    "Only pass this if you need to point somewhere else.",
+)
+@click.option(
+    "--aroma",
+    is_flag=True,
+    help="Include aroma regressors when cleaning functional time series.",
+)
+@click.option(
+    "--ndummy",
+    "n_dummy",
+    type=int,
+    help="Number of dummy scans at the beginning of the functional time series",
+    required=True,
+)
+@click.option(
+    "--tr",
+    "t_r",
+    type=float,
+    help="Repetition time of the functional time series",
+    required=True,
+)
+@click.option("--subject", type=str, default=None, help="Subject id.", required=True)
+@click.option(
+    "--session",
+    type=str,
+    default=None,
+    help="Session id.",
+)
+@click.option(
+    "--acquisition", type=str, default=None, help="Acquisition tag to filter scans by."
+)
+@click.option(
+    "--run",
+    type=str,
+    default=[],
+    help="Runs to use, pass once for each run. They will be concatenated.",
+    multiple=True,
+)
+@click.option(
+    "--echo",
+    type=str,
+    default=None,
+    help="Echo from dataset to generate target(s) for.",
+)
+@click.option(
+    "--nthreads",
+    type=int,
+    required=True,
+    help="Number of threads to run in parallel, you really don't want to wait on this to finish single threaded",
+)
+@click.option(
+    "--overwrite",
+    is_flag=True,
+    help="Overwrite existing outputs",
+)
+def run(
+    fmriprep_dir,
+    tedana_dir,
+    subjects_dir,
+    out_dir,
+    aroma,
+    n_dummy,
+    t_r,
+    subject,
+    session,
+    acquisition,
+    run,
+    echo,
+    nthreads,
+    overwrite,
+):
+    fmriprep_dir = Path(fmriprep_dir)
+    tedana = False
+    if tedana_dir is not None:
+        tedana = True
+        tedana_dir = Path(tedana_dir)
+        if not tedana_dir.exists():
+            raise FileNotFoundError(tedana_dir)
+
+    out_dir = Path(out_dir)
+    out_dir.mkdir(exist_ok=True, parents=True)
+
+    # transform anatomicals
+    tans_inputs_from_fmriprep(
+        fmriprep_dir, out_dir, subject=subject, overwrite=overwrite
+    )
+
+    bold_paths = []
+    # find the runs to use and create necessary inputs
+    if tedana:
+        # TODO: make confounds a passable option
+        if len(run) > 0:
+            for rr in run:
+                bold_paths.extend(
+                    find_bids_files(
+                        tedana_dir,
+                        type="func",
+                        sub=subject,
+                        ses=session,
+                        acq=acquisition,
+                        run=run,
+                        desc="optcomDenoised",
+                        suffix="bold",
+                        extension=".nii.gz",
+                    )
+                )
+        else:
+            bold_paths.extend(
+                find_bids_files(
+                    tedana_dir,
+                    type="func",
+                    sub=subject,
+                    ses=session,
+                    acq=acquisition,
+                    desc="optcomDenoised",
+                    suffix="bold",
+                    extension=".nii.gz",
+                )
+            )
+        for boldtd_path in bold_paths:
+            pfm_inputs_from_tedana(
+                boldtd_path,
+                fmriprep_dir,
+                tedana_dir,
+                out_dir,
+                aroma,
+                n_dummy,
+                t_r,
+                nthreads,
+                overwrite=overwrite,
+            )
+            # TODO: finish wiring up overwrite for everything below here
+    else:
+        if len(run) > 0:
+            for rr in run:
+                bold_paths.extend(
+                    find_bids_files(
+                        fmriprep_dir,
+                        type="func",
+                        sub=subject,
+                        ses=session,
+                        acq=acquisition,
+                        space="T1w",
+                        run=run,
+                        desc="optcomDenoised",
+                        suffix="bold",
+                        extension=".nii.gz",
+                    )
+                )
+        else:
+            bold_paths.extend(
+                find_bids_files(
+                    fmriprep_dir,
+                    type="func",
+                    sub=subject,
+                    ses=session,
+                    acq=acquisition,
+                    space="T1w",
+                    desc="optcomDenoised",
+                    suffix="bold",
+                    extension=".nii.gz",
+                )
+            )
+
+        # set the subjects dir
+        if subjects_dir is None:
+            subjects_dir = fmriprep_dir / "sourcedata/freesurfer"
+
+        if not subjects_dir.exists():
+            raise FileNotFoundError("Could not find subjects dir at {subjects_dir}")
+
+        for bold_path in bold_paths:
+            # TODO: fix pfm_inputs_from_fmriprep so that it uses the grey matter signal and not the global
+            confounds = [
+                "trans_x",
+                "trans_y",
+                "trans_z",
+                "rot_x",
+                "rot_y",
+                "rot_z",
+                "global_signal",
+            ]
+            pfm_inputs_from_fmriprep(
+                subject,
+                subjects_dir,
+                out_dir,
+                bold_path,
+                t_r,
+                n_dummy,
+                confounds=confounds,
+                aroma=aroma,
+            )
+
+    if session is not None:
+        pfm_indir_parent = out_dir / f"sub-{subject}/ses-{session}"
+    else:
+        pfm_indir_parent = out_dir / f"sub-{subject}/"
+
+    pfm_indir = build_pfm_inputdir(pfm_indir_parent, t_r, tedana=tedana)
+
+    pfm_out = pfm_indir_parent / "pfm_output"
+    pfm_out.mkdir(exist_ok=True, parents=True)
+
+    # get paths from config
+    config_path = Path.home() / ".contarg"
+    if not config_path.exists():
+        raise ValueError(
+            f"No contarg config found at {config_path}. Please run contarg tans config first."
+        )
+    config = configparser.ConfigParser()
+    config.read(config_path)
+    msc_path = config["TANS"]["MidnightScanClubPath"]
+    simnibs_path = config["TANS"]["SimNIBSPath"]
+    tans_path = config["TANS"]["TANSPath"]
+
+    pfm_script_path = write_pfm_script(
+        pfm_indir,
+        out_dir / f"sub-{subject}/",
+        pfm_out,
+        subject,
+        msc_path=msc_path,
+        tans_path=tans_path,
+        nthreads=nthreads,
+    )
+    pfm_script_path = f"'{pfm_script_path}'"
+
+    cmd = [
+        "matlab",
+        "-nodisplay",
+        "-nosplash",
+        "-r",
+        f"run({pfm_script_path}); exit",
+    ]
+    print(f"running {' '.join(cmd)}", flush=True)
+    subprocess.run(cmd, check=True)