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License: GNU General Public License v3.0
An automated and simple tool for fast quality analysis of animal MRI
License: GNU General Public License v3.0
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.
GIFS instead of images for the manual slice inspection
Goasting detection can be improved. For DTI scans
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.
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):
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
Line 468 in 9f54a86
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