Mental Illness and Neuroscience Discovery (MIND) Consortium Data
description
Transcript of Mental Illness and Neuroscience Discovery (MIND) Consortium Data
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Mental Illness and Neuroscience Discovery (MIND) Consortium Data
Randy L. Gollub, MD, PhD
Training Core PI, MGH
National Alliance for Medical Image Computing http://na-mic.org
This dataset in perspective
ClinicalN~380 subjects
Schizophrenics +Matched controls
ReliabilityN = 10
MGHDTI
National Alliance for Medical Image Computing http://na-mic.org
MIND Who? MIND Clinical Imaging Consortium (MCIC) Partner SitesMCIC) Partner Sites
Harvard/Massachusetts General HospitalHarvard/Massachusetts General Hospital University of New MexicoUniversity of New MexicoUniversity of MinnesotaUniversity of MinnesotaUniversity of IowaUniversity of Iowa
DOE Grant No. DE-FG02-99ER62764
National Alliance for Medical Image Computing http://na-mic.org
MIND MCIC Why?
A federally funded multi-site consortium created to advance our understanding of schizophrenia by supporting the acquisition of clinical, cognitive, genetic, morphometric, diffusion weighted and functional neuroimaging data from schizophrenia patients and matched controls using a common experimental protocol.
National Alliance for Medical Image Computing http://na-mic.org
MIND What?
• Two data sets– Reliability n =10 travelers to all 4 sites– Clinical n = 300+ Chronic and First
Episode (FE) schizophrenics and matched controls
• FE subjects and matched controls have follow-up data at 1 year (n = 46)
National Alliance for Medical Image Computing http://na-mic.org
MIND Reliability
• Healthy control subjects (n = 10, age 27-60, 5 female)
• Scanned twice at each site within 24 hour interval
• T1, T2, DTI, and 4 fMRI task paradigms
• Goal: calibrate for clinical study
National Alliance for Medical Image Computing http://na-mic.org
MIND Reliability DTI
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UNM 1.5 T Minnesota 3T Minnesota 3T Iowa 1.5 T MGH 1.5T SonataDTIR1 DTIR2
Data AcquisitionTR 9800 ms 10000 ms 11500 ms 9999 ms 8900 msTE 86 ms 97 ms 111 ms 71.8 ms 80 msBandwidth 1502 Hz 2170 Hz 1302 Hz 1860 Hz/PxVoxel Size 2x2 mm 2.5x2.5 mm 2x2 mm 1.875x1.875 2 x 2 mmSlice Thickness 2 mm 2 mm 2 mm 4mm/0mm gap 2 mmMatrix Size 128x128x64 128x128x64 128x128x64 128x128x34 128x128x64FOV 25.6x25.6 cm 32x32 cm 25.6x25.6 cm 24x24 25.6x25.6 cmNEX 4 2 2 2 1Scan Time 5 min 6:42 min 7:40 min 8 min 10:32 minSlice Prescription Parallel to AC-PC Axial Axial Axial Parallel to AC-PCPhase partial Fourier (6/8) (6/8) (6/8) Full (6/8)Raw filter On (weak) OFF OFF NA on
Image parameters 1Marix Size 128x128x64 128x128x64 128x128x64 128x128x64Resolution 2x2x2 mm 2.5x2.5x2 mm 2x2x2 mm 2x2x2 mm
Diffusion parametersDiffusion gradients 0, 1000 0, 1000 0, 1000 0, 250, 500, 750, 1000 0, 700Diffusion directions 6 12 12 6 60Directions in order taken (1,0,1) (1,0,0.5) (1,0,0.5) (0,0,1) { 1.0000000000, 0.0000000000, 0.0000000000 },
(-1,0,1) (0,0.5,1) (0,0.5,1) (1, 0, 0) { 0.5867917880, -0.3765825401, -0.7168409782 },(0,1,1) (0.5,1,0) (0.5,1,0) (0, 1, 0) { 0.8941946396, 0.0229172218, 0.4470914307 },(0,1,-1) (1,0.5,0) (1,0.5,0) (0.707, 0, 0.707) { 0.7292807003, -0.4109697317, 0.5470407112 },(1,1,0) (0,1.0,0.5) (0,1.0,0.5) (0, 0.707, 0.707) { -0.1542514872, 0.9643685389, -0.2149413870 },(-1,1,0) (0.5,0,1) (0.5,0,1) (0.707, 0.707, 0) { 0.1171358937, 0.7735388946, -0.6228296405 },
(1,0,-0.5) (1,0,-0.5) { -0.4075748558, -0.4149938010, -0.8134266298 },(0,-0.5,1) (0,-0.5,1) { 0.2113303675, 0.7537379261, 0.6222689246 },(-0.5,1,0) (-0.5,1,0) { 0.0953754479, -0.9695170076, 0.2256995700 },(1,-0.5,0) (1,-0.5,0) { -0.1354495929, -0.0334895243, -0.9902180869 },(0,1.0,-0.5) (0,1.0,-0.5) { -0.1421249090, -0.7505207879, -0.6453828764 },(-0.5,0,1) (-0.5,0,1) { -0.6370086516, 0.7461087590, -0.1937568003 },
{ 0.0805627090, 0.9716688439, 0.2221920516 },{ 0.1068711102, -0.0212132049, 0.9940465612 },
National Alliance for Medical Image Computing http://na-mic.org
MIND CICS
Over 300 subjects, Chronic and FE pts with matched controls
National Alliance for Medical Image Computing http://na-mic.org
MIND MCIC DTI
• Patients (FE + chronic) n = 115
• Controls n = 138
• Demographics available upon request
National Alliance for Medical Image Computing http://na-mic.org
MIND CICS DTI
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3T (Siemens Trio) Scan Parameters using 8-channel coil (UNM, UMN, UI)
T1 (Coronal, MPRAGE) T2 (Coronal, TSE) DTI1 DTI2
TR 2530 ms 10000 ms 10500 8000TE 3.79 14 98 83FA 7 149 IPAT=2TI 1100Bandwidth 181 193 1346 1302voxel size (x,y) 0.625x0.625 mm 0.625x0.625 mm 2.0x2.0 mm 2.5x2.5 mmslice thickness (z) 1.5 mm 1.8 mm 2.0 mm 2.0 mmmatrix size (x,y,z) 256x256x128 256x256x128 128x128x64 128x128x64FOV (x,y) ^ 16x16 cm ^ 16x16 cm 25.6x25.6 cm 32x32 cmNEX 1 1 2 3scan time * 11 min (each) * 9 min (each) 04:45 06:10Slice prescription Full brain coverage Full brain coverage Align parallel to ACPC Align parallel to ACPCPhase partial fourier 1 1 6/8 6/8Raw filter Off Off weak weakDiffusion directions n/a n/a 12 12
(MGH)T1
(Coronal, GRE) T2 (Coronal, TSE) DTI Field Map (Phase) Field Map (Magnitude)TR 12 9000 ms 9800 ms 1180 1180TE 4.76 64 86 10,14.76 10,14.76FA 20 180 n/a 90 90TI n/a n/a n/aBandwidth 110 149 1502 260 260voxel size (x,y,z) 0.625x0.625 0.625x0.625 2.0x2.0 mm 2.0x2.0 mm 2.0x2.0 mmslice thickness 1.5 mm 1.8 mm 2.0mm 2.0mm 2.0mmmatrix size (x,y,z) 256x256x128 256x256x128 128x128x64 128x128x64 128x128x64FOV (x,y) ^ 16x16 cm ^ 16x16 cm 25.6x25.6 cm 25.6x25.6 cm 25.6x25.6 cmNEX 3 2 4 1 1scan time 22 minutes 18 minutes 5 minutes 4 minutes 4 minutesSlice prescription Full brain coverage Full brain coverage Align parallel to ACPC Align parallel to ACPC Align parallel to ACPCPhase partial fourier 1 1 6/8 6/8 6/8Raw filter Off Off On (weak) Off OffDiffusion directions n/a n/a 6 n/a n/a
1.5 T (Siemens Sonata) Scan Parameters using 8-Channel Coil
National Alliance for Medical Image Computing http://na-mic.org
MIND CICS Preliminary Results
Freesurfer segmentation:
PutamenThalamus Hippocampus AmygdalaCaudate
Morrow, et al International Congress on Schizophrenia Research, 2007
National Alliance for Medical Image Computing http://na-mic.org
FreesurferHippocampal segmentation
1= Controls, 2= Chronic schizophrenia
Log normalized volume vs. age
National Alliance for Medical Image Computing http://na-mic.org
For Marty and Andy with
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Robust differences in fMRI activation indices between schizophrenic patients and controls Gollub et al, SFN 2007