March 3, 2005 mBIRN All Hands Meeting Data Provenance Nicole Aucoin.
UCI Progress MBIRN AHM. Progress Tool Development –FIPS and HID: Modifications to store derived...
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Transcript of UCI Progress MBIRN AHM. Progress Tool Development –FIPS and HID: Modifications to store derived...
UCI Progress
MBIRN AHM
Progress
• Tool Development– FIPS and HID: Modifications to store derived data,
including morphometric measures from Freesurfer• Methods Development
– DTI: Submitted paper: • Setsu Wakana, Arvind Caprihan, Martina M. Panzenboeck, Michelle Perry,
James H. Fallon, Randy L. Gollub, Kegang Hua, Jiangyang Zhang, Hangyi Jiang, Prachi Dubey, Ari Blitz, Peter van Zijl, Susumu Mori. 2006. Tractography-based Quantitative Analyses of White Matter Anatomy: Tracking Protocol, Reproducibility and Tract-Specific Quantification of Cerebral Hemisphere
• Tool Use– Segmentations of MCI 1.5T multisite dataset: 50
cases done from two sites and initial analyses begun
•22 subjects: Site 17
•Clinical Scores (above): MMSE, ADAS, CDR, BDI, Sex, Age, Years of Education
•Segmentation of one-time MRIs via Freesurfer to yield segmentation statistics (below).
Tool Use: Morphometric analyses of MCI data
Coefficients
20089.004 4101.258 4.898 .000-94.184 17.073 -1.186 -5.517 .000
-776.605 251.268 -2.854 -3.091 .009-1177.876 310.849 -.914 -3.789 .002
741.066 233.020 1.557 3.180 .0071180.511 401.171 .903 2.943 .011815.291 277.403 2.060 2.939 .012622.303 280.638 .929 2.217 .045
(Constant)AgeMMSEtotalCDRtnoboxMMSETimeOrientationMMSEPlaceOrientationMMSEAttentionMMSERecall
Equation 1B Std. Error
Unstandardized CoefficientsBeta t Sig.
• Utilizing multivariate regression analysis employing weighted squares, currently we are working on evaluating the effects of depressive symptoms on various parts of the MCI brain.
• Additionally, in an effort at theoretical detection and developing tools to aid in the MCI to AD conversion discriminate, we are developing algorithms that predict the volumes of various brain regions and circuits for a more comprehensive glimpse at the MCI / AD realm.
Lft Hippocampal Volume=20067.004-94.153(AGE)-776.604(MMSEtotal)-1177.874(CDRtnbox)+ 741.069(MMSEtimeortn)+1180.511(MMSEplaceortn)+ 815.291(MMSEattn)+622.303(MMSErecl)
Tool Use: Morphometric analyses of MCI data
To test the latest versions of Freesurfer
MBIRN Facilitations: Longitudinal Analysis
Getting a new Siemens 1.5T after a GE 1.5T: Replicate longitudinal analyses from Han, et al. 2006
*Test software compatibility with an external site
*Ensure correct version of Freesurfer/system compatibility
*Obtain updated version with support for mgz image format
Han X, Jovicich J, Salat D, van der Kouwe A, Quinn B, Czanner S, Busa E, Pacheco J, Albert M, Killiany R, Maguire P, Rosas D, Makris N, Dale A, Dickerson B, Fischl B. Reliability of MRI-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer. Neuroimage. 2006 Aug 1;32(1):180-94. Epub 2006 May 2.
*Freesurfer reconstruction using Han’s longitudinal program
*Acquire Global mean thickness values and surface thickness measures for variability comparisons
??
6 subjects across 8 scans, 4 sessions, and 2 scanners
GE scanner conversion to Siemens scanner
Reconstruction of T1 images with Freesurfer v. 3.0.3
Determine between session and within session variability
Preliminary results - GE only
MBIRN Facilitations: Longitudinal Analysis
Mean global thickness across sessions
1.95
2
2.05
2.1
2.15
2.2
2.25
2.3
2.35
2.4
2.45
1 2 3 4 5 6
subject
mea
n gl
obal
thic
knes
s (m
m)
subject
MBIRN-related collaborations
• FBIRN Group Analysis of morphometry using Freesurfer
Fig.1 Fig.2
-Fig.1: ‘Average’ subject w/ regions of t-ratios, above set threshold of 1.71.
-Fig.2: Plot of correlation between subject class and cortical thickness.
-ROI contains 159 vertices
- Areas of the left hemisphere in which controls showed thicker grey matter measures than did schizophrenic patients, in a dataset of schizophrenic (n= 13) and control (n= 12) each from UCI. Analyzed using Freesurfer. Submitted to ICOSR 2007.
DTI Study
slicetimernifti_tool
Fips-mc-fsl
Fips-sm2-fsl
Fips-stc-fsl
Fips-b0c-fsl
aTaskData
B0_mag
DerivedDataA
DerivedDataD
DerivedDataC
DerivedDataB
avwmergeavwmaths++mcflirtnifti_tool
mri_fwhmip_32Rnifti_tool
bet preludefugue fugueflirt fuguenifti_tool
FIPS_MBTS_preprocs
B0_phase
SourceData
DerivedData
Transform
Sub-transform
Legend