FreeSurfer: Individual Report

Summary

{% if summary.finished_at %} {% endif %} {% if summary.runtime_label %} {% endif %} {% if summary.fs_version %} {% endif %} {% if summary.fs_version_lastcall %} {% endif %} {% if summary.command %} {% endif %} {% if summary.talairach_rotation %} {{ summary.talairach_rotation }}{% if summary.talairach_rotation_flagged %} (large){% endif %} {% endif %} {% if summary.etiv_label %} {% endif %} {% if summary.brainseg_label %} {% endif %} {% if summary.edits %} {% endif %}
Subject{{ summary.subject }}
recon-all {{ summary.recon_status_label }}
Finished{{ summary.finished_at }}
Runtime{{ summary.runtime_label }}
FreeSurfer version{{ summary.fs_version }}
Last-call version{{ summary.fs_version_lastcall }}
Command{{ summary.command }}
Talairach check {{ summary.talairach_check_label }}
Talairach rotation
eTIV{{ summary.etiv_label }}
BrainSegVolNotVent{{ summary.brainseg_label }}
Edits{{ summary.edits|join(", ") }}
Report generated{{ summary.generated_at }}

Metrics

{% if metrics %}
{% if metrics.subject %}{% endif %} {% if 'wm_snr_orig' in metrics and metrics.wm_snr_orig is not none %}{% endif %} {% if 'gm_snr_orig' in metrics and metrics.gm_snr_orig is not none %}{% endif %} {% if 'wm_snr_norm' in metrics and metrics.wm_snr_norm is not none %}{% endif %} {% if 'gm_snr_norm' in metrics and metrics.gm_snr_norm is not none %}{% endif %} {% if 'cc_size' in metrics and metrics.cc_size is not none %}{% endif %} {% if 'holes_lh' in metrics and metrics.holes_lh is not none %}{% endif %} {% if 'holes_rh' in metrics and metrics.holes_rh is not none %}{% endif %} {% if 'defects_lh' in metrics and metrics.defects_lh is not none %}{% endif %} {% if 'defects_rh' in metrics and metrics.defects_rh is not none %}{% endif %} {% if 'topo_lh' in metrics and metrics.topo_lh is not none %}{% endif %} {% if 'topo_rh' in metrics and metrics.topo_rh is not none %}{% endif %} {% if 'con_snr_lh' in metrics and metrics.con_snr_lh is not none %}{% endif %} {% if 'con_snr_rh' in metrics and metrics.con_snr_rh is not none %}{% endif %} {% if 'rot_tal_x' in metrics and metrics.rot_tal_x is not none %}{% endif %} {% if 'rot_tal_y' in metrics and metrics.rot_tal_y is not none %}{% endif %} {% if 'rot_tal_z' in metrics and metrics.rot_tal_z is not none %}{% endif %}
Metric Value
Subject{{ metrics.subject }}
WM SNR (Original){{ "%.3f"|format(metrics.wm_snr_orig) }}
GM SNR (Original){{ "%.3f"|format(metrics.gm_snr_orig) }}
WM SNR (Normalized){{ "%.3f"|format(metrics.wm_snr_norm) }}
GM SNR (Normalized){{ "%.3f"|format(metrics.gm_snr_norm) }}
CC Size{{ "%.6f"|format(metrics.cc_size) }}
Holes (LH){{ metrics.holes_lh }}
Holes (RH){{ metrics.holes_rh }}
Defects (LH){{ metrics.defects_lh }}
Defects (RH){{ metrics.defects_rh }}
Topology (LH){{ "%.3f"|format(metrics.topo_lh) }}
Topology (RH){{ "%.3f"|format(metrics.topo_rh) }}
Contrast SNR (LH){{ "%.3f"|format(metrics.con_snr_lh) }}
Contrast SNR (RH){{ "%.3f"|format(metrics.con_snr_rh) }}
Rotation Tal X{{ "%.6f"|format(metrics.rot_tal_x) }}
Rotation Tal Y{{ "%.6f"|format(metrics.rot_tal_y) }}
Rotation Tal Z{{ "%.6f"|format(metrics.rot_tal_z) }}
{% else %}

No fsqc metrics.csv found next to this report. Re-run image generation, or copy the subject metrics.csv into the subject output directory.

{% endif %}

Talairach Registration

{% for item in tlrc %}
{% if ' {% endif %}
{% endfor %}

Aparc+Aseg Parcellations

{% for img_path in aseg %}

Click the mosaic to zoom. Drag to pan, scroll to zoom further, Esc to close.

Aparc+Aseg Parcellations
{% endfor %}

Surfaces

{% if surf_legend %} {% endif %}
{% for label, img_path in surf %}

{{ label }}

{{ label }}
{% endfor %}