neurita/boyle

Medical Image Conversion and Input/Output Tools

boyle's Issues

Add script to check if all subjects have the same file set.

e.g., check if all the subjects in a population have t1.nii.gz, diff.nii.gz, bvals...

If some don't, write a report with the differences.

Also put an Ipython notebook that shows file type distribution over subject groups.

Research: Detect if all images of one subject belongs to the same subject.

Given a set of images from different modalities, be able to infer if all the images belong to the same subject through image data.

Detect acquisition modality from DICOM file

Either from DICOM metadata or from image data.
From metadata it would be scanner-dependent I suppose.

Be able to detect what modality is a DICOM file/s: T1, T2, fMRI, DTI...

SCRIPT: Convert macuto/scripts/compare_id_sets.py into command line process

A script to acquire different types of lists of identifiers, e.g., folder names, PatientID values from DICOM files within a folder, a CSV file...

Then write a report comparing all the sets of identifiers.

Use exising folder!!!!

File "/opt/anaconda3/envs/medical-image/bin/inv", line 11, in
sys.exit(program.run())
File "/opt/anaconda3/envs/medical-image/lib/python3.6/site-packages/invoke/program.py", line 274, in run
self.execute()
File "/opt/anaconda3/envs/medical-image/lib/python3.6/site-packages/invoke/program.py", line 389, in execute
executor.execute(*self.tasks)
File "/opt/anaconda3/envs/medical-image/lib/python3.6/site-packages/invoke/executor.py", line 113, in execute
result = call.task(*args, **call.kwargs)
File "/opt/anaconda3/envs/medical-image/lib/python3.6/site-packages/invoke/tasks.py", line 111, in call
result = self.body(*args, **kwargs)
File "/home/oier/Projects/obesos/tasks.py", line 219, in split_dicoms_into_groups
copy_groups_to_folder(dcm_sets1, dest_dir, group_by_field)
File "/opt/anaconda3/envs/medical-image/lib/python3.6/site-packages/boyle-0.2.0-py3.6.egg/boyle/dicom/comparison.py", line 272, in copy_groups_to_folder
os.makedirs(folder_path, exist_ok=False)
File "/opt/anaconda3/envs/medical-image/lib/python3.6/os.py", line 220, in makedirs
mkdir(name, mode)

Filetype agnostic SubjectsSet instead of NiftiSubjectsSet in nifti/sets.py

We should create a set of subjects agnostic to the type of the image file.

rcfile.py host configuration should have priority over general configuration

rcfile.py host configuration variables should have priority over general configuration even for variables that do not exist in the general block or that have already been declared and used in the general block.

Pydicom should be in requirements

dicom module cannot be loaded if pydicom is not installed