aswendt-lab / aidaqc Goto Github PK

Parallel computing for subjects

Is your feature request related to a problem? Please describe.
the manual is hosted in a pdf, including details how to install the software.
by default, github will open the pdf internally without the option to copy text.
it makes copying the install commands bothersome.

Describe the solution you'd like
it would be more straight forward to have the install commands on the readme, so we can directly copy and paste it into our terminals.

Describe the bug
when using ParsingData.py on linux, i get.

PLOTTING QUALITY FEATURES...
findfont: Font family 'Times New Roman' not found.

I think this is because this font is not available.

To Reproduce
Steps to reproduce the behavior:

conda create -n aidaqc python=3.7 pip
conda activate

git clone https://github.com/Aswendt-Lab/AIDAqc.git
cd AIDAqc/
pip install -r requirements.txt

cd scripts/
chmod +x *.py
./ParsingData.py -i /project/4180000.36/aidaqc/bids -o project/4180000.36/aidaqc/test -f nifti

Expected behavior
I expect files to be generated in QCfigures. I don't get any. other files are there.

test/
|-- QCfigures
|-- caculated_features_anat.csv
|-- caculated_features_func.csv
|-- manual_slice_inspection
| |-- anat_anat_sub-0100100_ses-1_T2w_1.png
| |-- anat_anat_sub-0100101_ses-1_T2w_2.png
| |-- anat_anat_sub-0100102_ses-1_T2w_3.png
| |-- anat_anat_sub-0100103_ses-1_T2w_4.png
| |-- func_func_sub-0100100_ses-1_run-1_bold_1.png
| |-- func_func_sub-0100101_ses-1_run-1_bold_2.png
| |-- func_func_sub-0100102_ses-1_run-1_bold_3.png
| -- func_func_sub-0100103_ses-1_run-1_bold_4.png |-- nifti_data_addreses_anat.csv -- nifti_data_addreses_func.csv

Screenshots
na

Desktop (please complete the following information):

• OS: almalinux (also reproduced in an debian container)
• Browser
• Version 24.04

Additional context
times new roman is not a foss font, and it is not (easily) available on linux. i looked into different solutions (e.g. https://anaconda.org/conda-forge/mscorefonts and installing ttf-mscorefonts-installer in a container, but it did not work)

I think it is set there

Is your feature request related to a problem? Please describe.
installing locally is often a problem. software container (e.g. docker and apptainer) make software distribution easier.

Describe the solution you'd like
a dockerfile or apptainer definition file lets scientists build a working image of the software without having to worry about dependencies.

Goasting detection can be improved. For DTI scans

GIFS instead of images for the manual slice inspection