T1w image with grey background

Software Support
1

Hi everyone,
I saw similar issue here but the fix suggested did not help so I am posting again.
I wanted to plot statistical maps on MNI Pediatric template. I need a white background (black works as intended) however I get weird grey squares around the brain slices. As far as I know, the T1w image I have is fine, and it works if I use the default nilearn template. Passing the background image as path or a nifti object gives the same result.

import matplotlib.pyplot as plt
from nilearn.plotting import plot_stat_map, view_img
from nilearn.image import load_img
import os
from nilearn.glm import threshold_stats_img
from templateflow import api as tflow
import nibabel as nib

def plot_unc_figs(input_dir,output_dir):

    contrast = ['Go correct>0','Stop correct>0','Stop error>0','Stop error>Go correct','Stop correct>Go correct']
    grp = ['HC','OCD','OCD-HC']
    bg_ = '/mnt/projects/TECTO/nihpd_asym_04.5-18.5_nifti/nihpd_asym_04.5-18.5_t1w.nii'
    
    for i in contrast:
        
        for g in grp:
            
            zmap = load_img(os.path.join(input_dir,i,f'zmap_{i}_{g}.nii'))
            
            thresholded_map, threshold = threshold_stats_img(
                            zmap,
                            alpha=0.001,
                            height_control="fpr",
                            cluster_threshold=10,
                            two_sided=True,
                        )
            
            figure=plot_stat_map(thresholded_map,bg_img=bg_,draw_cross=False, black_bg=False, threshold=threshold)
            
            figure.savefig(os.path.join(output_dir,f'{i}_{g}.tiff'),dpi=300)
            
            display = view_img(thresholded_map,bg_img=bg_,draw_cross=False, black_bg=False, threshold=threshold)
            display.save_as_html(os.path.join(output_dir,f'{i}_{g}.html'))
            plt.close()
    

    
if __name__ == "__main__":
    input_dir ='/mnt/scratch/projects/TECTO/bids_func/derivatives/fmriprep/SecondLevel_25/acompcor'
    output_dir = '/mnt/projects/TECTO/SST_baseline_10_sep_2024/figures/fMRI/uncorrected'
    os.makedirs(output_dir,exist_ok=True)
    plot_unc_figs(input_dir,output_dir)

picture
picture1155×536 175 KB

Thank you.

Best,
Vytautas

2

I am unclear what you would expect to see?
can you show what the expected figure should look like?

however I get weird grey squares around the brain slices

not sure what you mean by this?

3

A head image with white background. Enabling black_bg, makes the whole area around the head black, which is nice, but how to make it work with white color? Is my only option a manual correction?

4

OK so it seems that this happens when the background image is not skull stripped.

A hack that can help: compute the brain mask of your background image and apply it before plotting:

from nilearn import datasets, plotting
from nilearn.maskers import NiftiMasker
from nilearn.masking import compute_brain_mask

subject_data = datasets.fetch_spm_auditory()

stat_img = datasets.load_sample_motor_activation_image()

# compute a rough mask for the brain and apply to only keep the brain
mask = compute_brain_mask(subject_data.anat)
masker = NiftiMasker(mask_img=mask)
tmp = masker.fit_transform(subject_data.anat)
masked_anat = masker.inverse_transform(tmp)

plotting.plot_stat_map(
    stat_img,
    threshold=3,
    title="original anat - black",
    bg_img=subject_data.anat,
    black_bg=True,
)

plotting.plot_stat_map(
    stat_img,
    threshold=3,
    title="original anat - not black",
    bg_img=subject_data.anat,
    black_bg=False,
)

plotting.plot_stat_map(
    stat_img,
    threshold=3,
    title="masked anat - black",
    bg_img=masked_anat,
    black_bg=True,
)

plotting.plot_stat_map(
    stat_img,
    threshold=3,
    title="masked anat - not black",
    bg_img=masked_anat,
    black_bg=False,
)

plotting.show()

image
image1469×851 195 KB

hope that helps