freesurfer_hipposf.ipynb 241 KB
Freesurfer Hippocampal Subfields
SUBJECTS_DIR = '../tests/subjects'
SUBJECT = 'bert'import os
from freesurfer_volume_reader.freesurfer import HippocampalSubfieldsVolumeFile
volume_files = list(filter(lambda f: f.subject == SUBJECT,
HippocampalSubfieldsVolumeFile.find(SUBJECTS_DIR)))
[os.path.basename(f.absolute_path) for f in volume_files]['lh.hippoSfVolumes-T1.v10.txt', 'lh.hippoSfVolumes-T1-T2.v10.txt']
import pandas
volume_frame = pandas.concat([f.read_volumes_dataframe() for f in volume_files])
volume_frame.head()| subfield | volume_mm^3 | subject | hemisphere | T1_input | analysis_id | |
|---|---|---|---|---|---|---|
| 0 | Hippocampal_tail | 123.456789 | bert | left | True | None |
| 1 | subiculum | 234.567891 | bert | left | True | None |
| 2 | CA1 | 34.567891 | bert | left | True | None |
| 3 | hippocampal-fissure | 345.678912 | bert | left | True | None |
| 4 | presubiculum | 456.789123 | bert | left | True | None |
sorted(volume_frame['subfield'].unique())['CA1', 'CA3', 'CA4', 'GC-ML-DG', 'HATA', 'Hippocampal_tail', 'Whole_hippocampus', 'fimbria', 'hippocampal-fissure', 'molecular_layer_HP', 'parasubiculum', 'presubiculum', 'subiculum']
list(volume_frame['analysis_id'].unique())[None, 'T2']
def generate_mode_label(row):
mri_sequences = ['T1' if row['T1_input'] else None,
row['analysis_id'].split('_')[0] if row['analysis_id'] else None]
return ' & '.join(filter(None, mri_sequences))
volume_frame['segmentation_mode'] = volume_frame.apply(generate_mode_label, axis=1)
volume_frame.to_csv('freesurfer_hipposf_volumes_{}.csv'.format(SUBJECT),
index=False)
volume_frame['segmentation_mode'].value_counts()T1 13 T1 & T2 13 Name: segmentation_mode, dtype: int64
volume_frame.pivot_table(values='volume_mm^3',
index=['subfield', 'hemisphere'],
columns='segmentation_mode')| segmentation_mode | T1 | T1 & T2 | |
|---|---|---|---|
| subfield | hemisphere | ||
| CA1 | left | 34.567891 | 44.567891 |
| CA3 | left | 678.912345 | 678.912445 |
| CA4 | left | 789.123456 | 789.124456 |
| GC-ML-DG | left | 567.891234 | 567.891244 |
| HATA | left | 91.234567 | 91.244567 |
| Hippocampal_tail | left | 123.456789 | 124.456789 |
| Whole_hippocampus | left | 1234.567899 | 1244.567899 |
| fimbria | left | 89.123456 | 89.124456 |
| hippocampal-fissure | left | 345.678912 | 445.678912 |
| molecular_layer_HP | left | 56.789123 | 56.789124 |
| parasubiculum | left | 45.678912 | 45.678912 |
| presubiculum | left | 456.789123 | 456.789124 |
| subiculum | left | 234.567891 | 244.567891 |
%matplotlib notebook
from matplotlib import pyplot
import seaborn
ax = seaborn.barplot(data=volume_frame[volume_frame['subfield'] == 'Whole_hippocampus'],
x='hemisphere',
y='volume_mm^3',
hue='segmentation_mode')
ax.set_title('Hippocampal Volume of Subject {}'.format(SUBJECT))
ax.legend(loc='lower right')
<matplotlib.legend.Legend at 0x7f04334ae4a8>
subfield_volume_frame = volume_frame[volume_frame['subfield'] != 'Whole_hippocampus']
pyplot.figure()
seaborn.set(font_scale=0.8)
ax = seaborn.barplot(data=subfield_volume_frame[subfield_volume_frame['hemisphere'] == 'left'],
x='subfield',
y='volume_mm^3',
hue='segmentation_mode')
ax.set_xticklabels(ax.get_xticklabels(), rotation=60)
ax.set_title('Hippocampal Subfield Volumes of Subject {}\nLeft Hemisphere'.format(SUBJECT))
Text(0.5, 1.0, 'Hippocampal Subfield Volumes of Subject bert\nLeft Hemisphere')