gen_report.py

from pathlib import Path
from bids import BIDSLayout
from nibabel.freesurfer.mghformat import load
from nireports.assembler.report import Report
import numpy as np
import nibabel as nib
from nilearn import plotting

def gen_subj_fs_report(fs_dir, subj, outdir):
    subj_fs_dir = Path(fs_dir) / subj
    hemis = ["lh", "rh"]
    stypes = ["inflated", "pial", "white", "midthickness"]
    surfs = {f"{hemi}_{stype}": subj_fs_dir / "surf" / f"{hemi}.{stype}" for hemi in hemis for stype in stypes}
    print(surfs)

# fs_dir = "/mnt/projects/nireports/nireports_freesurfer/bids_testset/derivatives/freesurfer"
# subj = "sub-pp001"
# outdir = "/mnt/projects/nireports/nireports_freesurfer/reportlets"
# gen_subj_fs_report(fs_dir, subj, outdir)

entities = {'session': '01', 'subject': 'pp001', 'suffix': 'T1w'}

bootstrap_file=f"/mnt/projects/nireports/nireports_freesurfer/bootstrap_data/bootstrap-fs.yml"
prov = {}

prov["Freesurfer build stamp"] = f"freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275"
prov["Execution environment"] = f"Linux d4ef45c6cca2 5.14.0-1057-oem #64-Ubuntu"

fs_metrics = {'vol_mm3_region3rd-Ventricle': '805.0', 'vol_mm3_region4th-Ventricle': '1439.9', 'vol_mm3_region5th-Ventricle': '0.0', 'vol_mm3_regionBrain-Stem': '19420.3', 'vol_mm3_regionCC_Anterior': '985.3', 'vol_mm3_regionCC_Central': '712.0', 'vol_mm3_regionCC_Mid_Anterior': '880.1', 'vol_mm3_regionCC_Mid_Posterior': '639.3', 'vol_mm3_regionCC_Posterior': '1024.8', 'vol_mm3_regionCSF': '1036.4', 'vol_mm3_regionLeft-Accumbens-area': '448.2', 'vol_mm3_regionLeft-Amygdala': '1590.8', 'vol_mm3_regionLeft-Caudate': '3564.4', 'vol_mm3_regionLeft-Cerebellum-Cortex': '56219.8', 'vol_mm3_regionLeft-Cerebellum-White-Matter': '12602.0', 'vol_mm3_regionLeft-Hippocampus': '3536.5', 'vol_mm3_regionLeft-Inf-Lat-Vent': '485.5', 'vol_mm3_regionLeft-Lateral-Ventricle': '7887.5', 'vol_mm3_regionLeft-Pallidum': '1827.0', 'vol_mm3_regionLeft-Putamen': '4689.9', 'vol_mm3_regionLeft-Thalamus': '7665.0', 'vol_mm3_regionLeft-VentralDC': '3840.2', 'vol_mm3_regionLeft-WM-hypointensities': '0.0', 'vol_mm3_regionLeft-choroid-plexus': '512.2', 'vol_mm3_regionLeft-non-WM-hypointensities': '0.0', 'vol_mm3_regionLeft-vessel': '29.0', 'vol_mm3_regionOptic-Chiasm': '105.7', 'vol_mm3_regionRight-Accumbens-area': '463.9', 'vol_mm3_regionRight-Amygdala': '1612.5', 'vol_mm3_regionRight-Caudate': '3432.6', 'vol_mm3_regionRight-Cerebellum-Cortex': '57641.0', 'vol_mm3_regionRight-Cerebellum-White-Matter': '11853.5', 'vol_mm3_regionRight-Hippocampus': '3959.4', 'vol_mm3_regionRight-Inf-Lat-Vent': '160.2', 'vol_mm3_regionRight-Lateral-Ventricle': '5654.4', 'vol_mm3_regionRight-Pallidum': '1825.9', 'vol_mm3_regionRight-Putamen': '4690.0', 'vol_mm3_regionRight-Thalamus': '7954.8', 'vol_mm3_regionRight-VentralDC': '3562.0', 'vol_mm3_regionRight-WM-hypointensities': '0.0', 'vol_mm3_regionRight-choroid-plexus': '400.7', 'vol_mm3_regionRight-non-WM-hypointensities': '0.0', 'vol_mm3_regionRight-vessel': '16.0', 'vol_mm3_regionWM-hypointensities': '343.6', 'vol_mm3_regionnon-WM-hypointensities': '0.0'}

metadata={
    "dataset": "Test dataset Freesurfer report",
    "fs-metadata": {
        "Provenance Information": prov,
        "Metrics": fs_metrics,
    }
}

output_dir = "fs_report"
uuid = "random_uuid"
reportlets_dir = "reportlets/sub-pp001/ses-01/figures"

robj = Report(output_dir, uuid, reportlets_dir=reportlets_dir,
              bootstrap_file=bootstrap_file, metadata=metadata,
              plugin_meta={}, **entities)

robj.generate_report()