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PPMI Resting State and T1-Standardization projects
Darren Gitelman (NU) Xue Wang (NU)
Todd Parrish (NU) Petros Petrosyan (LONI)
Ivo Dinov (LONI) Alen Zamanyan (LONI) Karen Crawford (LONI)
Tanya Simuni (NU) John Seibyl (MNI) Arthur Toga (LONI)
Bret Borowski (Mayo)
Resting State Project: scan numbers
• Only 3/8 sites approved for amendment 8 (in the past year), which allowed later scanning of controls
Group # baseline scans Repeat studies
Control 10 4- 2x PD 97 52- 2x, 4- 3x SWEDD 14 3- 2x Prodromal 15 1- 2x GenCohort PD 1 GenCohort Unaff. 7
Resting state project: quality measures
PD (n=97) Mean ± StDev
Control (n=10) SWEDD (n=14)
Age 61.0 ± 10.19 66.6 ± 7.15 62.8 ± 9.32
Gender 68 M / 29 F 9 M / 1 F 9 M / 5 F
Scan QC: Good 40 5 3
Scan QC: Questionable
49 2 7
Scan QC: Bad 8 3 4
Resting State fMRI: scans by site
Sites
Scan
s
0
5
10
15
20
25
1 2 3 4 5 6 7 8
Control
PD
QC parameters
rsfMRI: Control vs. PD FD (mm) ( < 0.5)
DVARS ( < 50)
TEMP- SNR ( > 120)
Control (n=10) 1.14 ± 0.58 62.90 ± 10.95 120.31 ± 18.10
Parkinsons (n=97) 1.06 ± 0.77 58.42 ± 18.48 133.64 ± 22.20
Framewise displacement
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0
Bad Questionable Good
Control Parkinsons
DVARS
0
10
20
30
40
50
60
70
80
Bad Questionable Good
Control Parkinsons
Temporal SNR
0
20
40
60
80
100
120
140
160
Bad Questionable Good
Control Parkinsons
Resting State fMRI: QC by Site
0
2
4
6
8
10
12
14
16
18
1 2 3 4 5 6 7 8
Bad
Good
Questionable
Sites
Scan
s
Resting State Project
• Reduced data quality nearly always related to subject movement – Make subjects as comfortable as possible. – Cushion their head to minimize movement. – Instruct them often not to move, even before
each scan (especially resting state and DTI) • Resting state sites: get approval for
Amendment 8!! • Plan for control scans when subjects return
T1 standardization
• Goal: To acquire standardized, research quality T1 MRI data at all sites. (stop throwing away data)
• T1 MRI scans now standardized using ADNI sequences across all PPMI sites (n=33). (Thanks to ADNI!)
• T1 MRI scans now undergoing quality review
• Sites received a compressed folder containing the
sequences to be uploaded and a run sheet
T1 standardization files
PPMI MRI Operations Manual v7.0 20JAN2015.FINAL
MRI Sequence installation
1. Read the manual for your scanner type
2. Unzip the compressed sequence file and copy to a clean (virus free) flash drive
3. Read the manual again and follow the directions for sequence installation.
MRI scanning protocols
• We encourage all sites to upgrade to 3T if possible. Inform IND if any scanner changes.
• Protocols – Non-DTI (non-resting state) MRI sites (non-Prisma) – DTI (± RS) sites (non-Prisma) – Prisma sites
Non-DTI (non-RS) sites (non-Prisma) • Site was previously not a designated DTI site (GE, Philips, some
Siemens) • Install and run only ADNI-based sequences (T1 and T2)
HUMAN •MPRAGE SENSE2 (ADNI parameters: 1 x 1 x 1.2 mm3 ) •Axial T2-FLAIR •Axial T2-TSE with Fat Sat
PHANTOM Run just 1 time after the ADNI sequences have been installed. Do not run the phantom for every subject.
DTI (± RS) sites (non-Prisma)
• Site was previously a designated DTI site (Siemens Trio, Verio)
• Install ADNI-based sequences (T1)
• Run both PPMI and ADNI sequences
DTI (± RS) sites (non-PRISMA) PPMI Sequences (What the site has been running) HUMAN • DTI_gated • MPRAGE GRAPPA (original PPMI parameters: 1 x 1 x 1 mm3) • ep2d_Resting_State • Axial PD-T2 TSE FS • DTI_gated
PHANTOM (Should be run on days when subject MRI scans are obtained.) • DTI • ep2d_resting_state
ADNI Sequences (New additional sequence) HUMAN • MPRAGE GRAPPA 2 (ADNI parameters: 1 x 1 x 1.2 mm3 )
PHANTOM Run just 1 time after the ADNI sequences have been installed.
Prisma Sites
• Install and run the protocol file provided by PPMI (includes both PPMI and ADNI sequences)
T1 Standardization Quality Control
T1 Standardization Quality Control
The End
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