NeuroBook From Mengfei
1
Preface
2
Introduction
3
Programming and Utility codes
3.1
Tips for Neuroimage processing
3.2
Useful Regex examples
3.3
Useful Shell commands and examples
3.3.1
Find files and copy to target folder
3.3.2
Kill a range of running batch jobs
3.3.3
sed
3.3.4
tr
3.3.5
Batch job submit
3.3.6
Copy files after checking file existence
3.4
ITK_SNAP command line tutorials
3.4.1
ITK-SNAP open serial images once for all
3.5
Compress files/folders with gzip and tar
3.6
Most commonly used codes
3.7
PPMI ppmi_tractseg_job_extract_freewater
4
Structural Neuroimaging
4.1
DICOM to Nifti conversion
4.2
Conversion jobs for Caixin DICOM files
4.3
T1 Volume calculation
4.4
Deep and Periventricular white matter separation
4.5
Reslice/resample the Images
4.6
Obtain the overlap mask from Two Images
4.7
Regsitration
4.7.1
WM/GM/WMH registration into IVIM space
4.7.2
Register WMH into MNI space
4.8
Segmentation
4.8.1
Lesion Segment Tool (LST)
4.8.2
SAMSEG
4.8.3
SAMSEG tiv and regional volume extraction
4.9
BIANCA
4.10
WMH seg by LST_AI
4.11
Difference images
4.12
FLAIR in MNI space
4.13
Acapulco Cerebellum segmentation
4.14
Acapulco cerebellar volume extraction
4.15
sc-limbic segementation
5
Network Analysis
5.1
BrainNet Viewer
6
Diffusion MRI
6.1
DWI pre-processing
6.2
DWI pre-processing with synthesized b0
6.3
PSMD calculation and extraction
6.4
Extract 3D volumes from 4D volumes
6.5
Tractseg pipeline
6.6
Tractseg FA_MD metrics extraction
6.7
Freewater pipeline
6.8
Free water in T1 longitudinal space
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Mengfei NeuroBook
Chapter 5
Network Analysis
5.1
BrainNet Viewer