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

• 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

Scans

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

10 20 30 40 50 60 70 80 Bad Questionable Good

Control Parkinsons

Temporal SNR

20 40 60 80 100 120 140 160

Bad Questionable Good

Control Parkinsons

Resting State fMRI: QC by Site

2 4 6 8 10 12 14 16 18 1 2 3 4 5 6 7 8

Bad Good Questionable

Sites

Scans

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