ilkayisik

from nilearn.plotting import plot_glass_brain
fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(10, 12))
for gidx, roi in enumerate(rois):
    plot_glass_brain(roi, plot_abs=False, symmetric_cbar=False,
        black_bg=True, display_mode='lyrz', colorbar=True, axes=axes[gidx],
        title=roi_ids[gidx])
plt.savefig(savepath + 'glass_summary.png', dpi=300)

ilkayisik

root=pat/to/root
cd ${root}
for tiffile in *.tif; do
  echo $tiffile
  in_file=${tiffile}
  out_file=${in_file%.*}_whitebg.tif
  convert -fill white -opaque black ${in_file} ${out_file}
done

ilkayisik

for sub in {01..26}; do
  echo sub-${sub}
  mkdir /Users/ilkay.isik/MPI-Documents/hack_19/data/analysis/sub-${sub}
  mkdir /Users/ilkay.isik/MPI-Documents/hack_19/data/analysis/sub-${sub}/pfobloc
  src=/Users/ilkay.isik/project_folder_temp/fc_content/MRI_data/lscp_data/derivatives/analysis/sub-${sub}/pfobloc/pfobloc.feat
  
  dest=/Users/ilkay.isik/MPI-Documents/hack_19/data/analysis/sub-${sub}/pfobloc/pfobloc.feat
  echo ${src} '****' ${dest}
  cp -r ${src} ${dest}
done

ilkayisik

import matplotlib.pyplot as plt
import seaborn as sns

for s in range(nr_subjects):
    fig, ax = plt.subplots(5, 6, sharex=True, sharey=True, figsize=(15, 20))
    sns.despine()
    ax = ax.flatten()
    for m in range(nr_movies):
        ax[m].plot(cdt[s, m, :])
        ax[m].plot(cdrt[s, m, :])

ilkayisik

var="hello/my/name/is"

# everything after the first slash:
echo "${var#*/}"

# everything after the last slash:
echo "${var##*/}"

# everything before the first slash:
echo "${var%%/*}"

ilkayisik

# to be used to save jupyter notebooks as html files
import os
from ilkay_tools.jupyter_save import save_nb, output_html
import time

%%javascript
IPython.notebook.kernel.execute(`notebookName = '${IPython.notebook.notebook_name}'`);

nb_fdir = os.getcwd()
nb_name = notebookName.split('.', 1)[0] # discard the extension

ilkayisik

root='/Users/ilkay.isik/project_folder_temp/fc_content/MRI_data/lscp_data/derivatives'
input=path/to/2mm_input.nii
output=path_to_1mm_output.nii
ref=path_to_1mm_ref.nii
c3d ${ref} ${input} -int 0 -reslice-identity -o ${output}

ilkayisik

for fname_full in $(ls $sub_ses/prepro/source_files/*.nii); do

ilkayisik

from glob import glob

sub_exc = [0, 1, 2, 15, 18]
sub_list = ['sub-{:02d}'.format(s+1) for s in sub_exc]
files1 = [i for i in files1 if i.rsplit('analysis/',1 )[1].split('/')[0] not in sub_list]
files2 = [i for i in files2 if i.rsplit('analysis/',1 )[1].split('/')[0] not in sub_list]
files3 = [i for i in files3 if i.rsplit('analysis/',1 )[1].split('/')[0] not in sub_list]


files = [files1, files2, files3]

ilkayisik

tksurferfv fsaverage lh inflated -aparc -overlay sig.mgh -fminmax 2 3