PPMI Resting State and T1-Standardization projects Darren Gitelman - PowerPoint PPT Presentation

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 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 • Only 3/8 sites approved for amendment 8 (in the past year), which allowed later scanning of controls

Resting state project: quality measures PD (n=97) Control (n=10) SWEDD (n=14) Mean ± StDev 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: 49 2 7 Questionable Scan QC: Bad 8 3 4

Resting State fMRI: scans by site 25 20 Scans 15 Control PD 10 5 0 1 2 3 4 5 6 7 8 Sites

QC parameters

rsfMRI: Control vs. PD FD (mm) DVARS TEMP- SNR ( < 0.5) ( < 50) ( > 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 2.0 1.8 1.6 1.4 1.2 1.0 0.8 0.6 0.4 0.2 0.0 Bad Questionable Good Control Parkinsons

DVARS 80 70 60 50 40 30 20 10 0 Bad Questionable Good Control Parkinsons

Temporal SNR 160 140 120 100 80 60 40 20 0 Bad Questionable Good Control Parkinsons

Resting State fMRI: QC by Site 18 16 14 12 Scans 10 Bad Good 8 Questionable 6 4 2 0 1 2 3 4 5 6 7 8 Sites

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 mm 3 ) • 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 mm 3 ) • 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 mm 3 ) 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

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