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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)

PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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Page 1: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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)

Page 2: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 3: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 4: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 5: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

QC parameters

Page 6: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI 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

Page 7: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 8: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

DVARS

0

10

20

30

40

50

60

70

80

Bad Questionable Good

Control Parkinsons

Page 9: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

Temporal SNR

0

20

40

60

80

100

120

140

160

Bad Questionable Good

Control Parkinsons

Page 10: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 11: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 12: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 13: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

T1 standardization files

Page 14: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:
Page 15: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

PPMI MRI Operations Manual v7.0 20JAN2015.FINAL

Page 16: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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.

Page 17: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 18: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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.

Page 19: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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

Page 20: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

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.

Page 21: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

Prisma Sites

• Install and run the protocol file provided by PPMI (includes both PPMI and ADNI sequences)

Page 22: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

T1 Standardization Quality Control

Page 23: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

T1 Standardization Quality Control

Page 24: PPMI Resting State and T1-Standardization projects · 6/4/2015  · PPMI Sequences (What the site has been running) HUMAN •DTI_gated •MPRAGE GRAPPA (original PPMI parameters:

The End