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navona

navona

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NM_07_hierarchicalClustering
NM_06_CCA
NM_05_correlations
NM_04_sanityChecks
NM_03_dataCorrection
NM_02_medication
NM_01_dataCleaning
Clustering and cut-off for CCA CV1 X scores
PAC_6
NM-MRI CCA prediction
NM-MRI: Hierarchical clustering CCA LC and cognition (CV1)
CCA analysis: SPINS GE Discovery and Siemens PRISMA sites
Corpus Callosum fibers (UKF)
SPINS UKF: Fibre measurement summary
NM-MRI LC masks
PLSC (symmetrical correlation PLS)
Human phantoms
SPINS & PNS CONSORT
CCA sensitivity
Review of scog and ncog distributions
CCA
Review and remove confounds
Review and impose normality
Review and remove outliers
SPINS and PNS automated QC
SPINS and PNS CMH GE MRI: Fibre measurement summary
Finding lost tracts (IOFF)
SPINS and PNS -- participant munging
SPINS DWI-to-tractography: GE vs. Siemens
SPINS tractography fibre measurement summary (BrainSuite distortion correction and RAS bvecs)
BrainSuite distortion correction and RAS bvecs: Summary
BrainSuite distortion correction and RAS bvecs: TOIs
BrainSuite distortion correction and RAS bvecs: Registration
BrainSuite distortion correction and RAS bvecs: Tractography
Eddy vs. BrainSuite bvec comparison
Review 2 of 3: Slicer tractography
SPINS Review 1 of 3: Preprocessing
WMA review: Comparison of custom vs. ORG atlas on select SPINS participants
WMA review: SPINS parcellation (non)success
WMA review: Visualization of the left ILF
WMA review: Visualization of the right ILF
WMA review: Visualization of the right UF
WMA review: Visualization of the left UF
WMA review: Registration to the ORG atlas
WMA review: Visualization of the right AF
WMA review: Visualization of the left AF
SPINS test subjects: whole brain tracts (current parameters)
SPINS CCA analysis: smaller feature set
SPINS: Neurocognition and social cognition outliers by SD
PAC Meeting 3 Report [Navona Calarco 2020-01-27]
SPINS: Review of brain extraction (BET) for matched RISH participants
SPINS: FA site/scanner effect (pre-harmonization)
SPINS: Review multivariate and univariate normality of CCA `Y` set (neurocognition and social cognition)
SPINS: Review outliers of CCA `Y` set (neurocognition and social cognition)
SPINS: Review multivariate and univariate normality of Slicer FA values
NEEDS REVIEWED BY AV
Automated QC of SPINS DWI with `eddy quad` and `MRTrix`
SPINS: Review of QC metrics from `eddy` and `MRTrix`
SPINS CCA: Missing data interpolation – fibre measurements
SPINS CCA: Missing data interpolation – clinical
SENDEP apathy and LC CNR
SENDEP distributions of apathy-related items
SPINS CCA analysis sample characteristics
SPINS tractography fibre measurement summary (Slicer)
SPINS SSD Psychotropic Medications
Need input from AV before finalized
Tracts available in Slicer (n=41)
SPINS calculation of CPZE using `chlorpromazineR` package
RISH matched participant visualizations
CONSORT-style participant flow diagram
RISH harmonization -- final participant matching
Using human phantoms
PSYC2002 final assignment
Derivate scores (CNR/volume) for SN and LC
Curage TMT A & B
Analysis of SN NM across LLD and HC groups
Analysis of LC NM across LLD and HC groups
Methods: NM in the Substantia Nigra (SN)
Methods: NM in the Locus Coeruleus (LC)
Estimating omega and CI for categorical data
CCA: missing values ... unrobust correlation matrix ... negative eigenvalues
PSY2002 Assignment 4 (SEM)
PSY2002 Assignment 3 (LDA)
PSY2002 Assignment 2 (CCA)
PSY2002 Assignment 1 (PCA)
Comparison of SN binarization thresholds
This document correctly uses 4mm as the reference ROI selection radius.
Comparison of SN reference ROI circle size
Comparison of SN binarization thresholds
Note: this analysis was done with an incorrect reference ROI of 5 radians (should be 4 radians). Correct analysis is at http://rpubs.com/navona/NM_SN_thresholds_4mm
Calculation of SN across multiple slices
RISH_matching_CMH-ZHP
RISH_matching_CMH-MRP
RISH_matching_CMH-MRC
Review of FSL eddy's slice-to-volume correction
SPINS EA and circles accuracy
SPINS circles video ratings
SPINS EA video ratings
SPINS participant matching: MRC & MRP
This is a test - reference site will ultimately be CMH. Note: participants were not matched on the basis of handedness
DWI QC: inter-rater agreement review (POND; N=99)
SPINS participant matching
DWI QC: inter-rater agreement review (POND; N=30)
SPINS raw FA values across sites
Thesis report - week 2
Slicer
Thesis report - week 1
TBSS
SCWG feedback
Example .html document summarizing attendee feedback for the CAMH Scientific Computing Working Group (SCWG). Data is from May 2017.
Trivia Pilot (knowledge & curiosity)
[SPINS] XBRAIN RS biotypes
[SPINS] participant MRI counts (2018-07-22)
[OPT] call report (2018-05-17)
[SPINS] travelling phantom analysis
Year 4 travelling human phantoms at ToNI.
[OPT] review of early ToNI MRIs
[SPINS] comparison of PRISMA scanners