tigrlab / dmripreproc Goto Github PK

https://miykael.github.io/nipype_tutorial/notebooks/advanced_sphinx_ext.html

• upsample factor -> feed in to mrresize
• list of nodes to optionally ignore: denoise, unring, fieldmaps

should contain:

• FSL 6.0.1
• Freesurfer 6.0
• ANTS
• MRtrix3
• Python 3

Resources:

• https://blog.docker.com/2019/07/intro-guide-to-dockerfile-best-practices/
• https://github.com/kaczmarj/neurodocker
• https://github.com/BIDS-Apps/dockerfile-templates

• descriptor
• invocation

More information on derivatives found here:

https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/edit#heading=h.bwu2pvc2fsuj

https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60/edit#heading=h.mqkmyp254xh6

Diffusion Preprocessing

• check skull stripping of b0

Susceptibility Distortion Correction

fieldmap, phasediff, phase

• check skull stripping of magnitude image
• check registration of fieldmap image to b0

topup

synthetic b0

• overlay synthetic b0 over T1 (synthetic b0 might misclassify some CSF above brain as part of white matter in cortex)

all

• overlay white matter mask over eddy corrected b0
• gif of uncorrected vs eddy corrected b0

Eddy

• link to eddy_quad pdf
• calculate framewise displacement?
• visualize CSD residuals

Tensor

• visualize tensor directions using V1 image
• visualize tensor residuals (still relevant?)

Tractography

• visualize grey-white matter interface

add additional options for slice-to-volume motion correction

migrate or contribute to sdcflows

templateflow