0rc0 / neuromet_mp2rage_pypes

Pipelines for structural analysis for NeuroMet Project

NeuroMET MP2RAGE pipeline

Structural preprocesing pipeline for MP2Rage

The pipeline

The T1w_UNI image from the MP2Rage sequence has an optimal contrast for the brain, but its high background noise, caused by the high (7 T) magnetic field, makes it difficult to use this image as-is with various software packages. On the other hand, the T1w denoised (T1w_DEN) image loses contrast with the denoising process. This pipeline processes the T1w images to achieve an image with the brain from the UNI image and the background from DEN image and thus an optimal contrast.

Usage

See Example Notebook. Only the variables in Settings section should be modified.

neuromet_mp2rage_pypes's Issues

Freesurfer directory has not the _T1 or _T2 suffix

the final freesurfer path is i.e.

NeuroMet2004.freesurfer

but it should be something like

NeuroMet2004_T1.freesurfer

The Pipeline should take a BIDS directory structure as input

The Pipeline should take a BIDS directory structure as input

Adjust Volumes

Adjust Volumes as in attachment
3_adjust_Volumes_To_TIV_Rscript.R.txt

get_mask should be a node

UNIbrainDENskull is not connected to sink anymore

UNIbrainDENskull is not saved anymore in destination directory

The SPM segmentation for UNI and DEN should be not in different workflows

There should be an iterable for ['UNI','DEN']

i.e.:
https://miykael.github.io/nipype_tutorial/notebooks/basic_iteration.html

same as:
0rC0/NeuroMet_Structural_analysis#3

README.md

write a README.md

The Jupyter notebook should be executable out-of-the-box with test data

The Jupyter notebook should be executable out-of-the-box with data in test data folder

Integrate quantification in Workflow

Use better node names in workflow

as object