enigma ocd working group teleconference 19 th of february 2015 2 pm gmt (greenwich mean time)...
TRANSCRIPT
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ENIGMA OCD working group
Teleconference 19th of February 2015
2 PM GMT (Greenwich Mean Time) Amsterdam/Barcelona/Berlin/Zurich/Munchen/Rome/Milan 3 PM
Sao Paulo noonTokyo/Kyoto/Seoul 11 PM
Cape Town 2 PMLos Angeles 6 AM
New York/Toronto/Michigan/Boston 9 AMBangalore 7.30 PM
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses3. draft form analysis plans, for additional subcortical meta-analyses4. preparation mega-analyses on pooled raw data5. expert-subgroups for specific topics/analyses6. funding7. status GWAS8. future meetings
Please, send me ([email protected]) an email as soon as your site ‘on the line’, with the name of the person representing the site during the TC.
Take care of the quality of the TC: (un)mute your line by pressing 16!!
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Agenda1. status subcortical meta-analyses
1. Quality control guidelines2. Putamen / pallidum segmentations (comparison alternatives)3. Status per site and overall overview
2. planning cortical meta-analyses3. draft form analysis plans, for additional subcortical meta-
analyses4. preparation mega-analyses on pooled raw data5. expert-subgroups for specific topics/analyses6. funding7. status GWAS8. future meetings
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Subcortical segmentations FreeSurferQuality Check Important to verify that the FreeSurfer
reconstructions are free from errors and excluded if necessary
Look at histograms find corresponding outliers in LandRVolumes
and evaluate segmentation Perform outlier detection
Note that, an outlier does not automatically means a bad segmentation
Quality check with webpages
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A few examples of bad segmentations cover• The shape of the structure is not
delineated properly• Part of the segmentation of one structure
overlaps with that of another adjacent structure
• Part of the structure is left out• Asymmetrical delineation
note that if a subject has skewed head position in the scanner, the structures may appear asymmetrical while they are in fact not
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Shape of the structure is not delineated properly
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Overlapping structuresSegmented pallidum overlapswith putamen
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Part of the structure is left out
Parts of the bilateral putamenare left out
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Asymmetrical delineation
Asymmetrical, butskewed head position
Asymmetrical, badsegmentation
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Tips for quality checking Always verify poor segmentations in
FSLview FSLview gives you a 3D representation instead
of a 2D (improving your judgment) Adjust contrasts (T1 and segmentation colors)
to evaluate segmentations
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Issue: Pallidum segmentationsFreeSurfer
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Issue: Putamen segmentationsFreeSurfer
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Putamen and pallidum segmentationsFreeSurfer 5.0 vs 5.3
• overall quality approximately equal (in favor of FreeSurfer 5.3)• not always the same subjects get excluded in both versions• repeated in other datasets (1.5T and outside VUmc Amsterdam)
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FSL First vs FreeSurfer 5.3 FIRST is a model-based segmentation tool The shape models used in FIRST are
constructed from manually segmented images
Before segmentation images were ‘neckcropped’ and ‘skullstripped’ using BET
While making the quality check webpages for FIRST, images are normalized to standard MNI space
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Putamen and pallidum segmentations FIRST
• Overall quality improved with FIRST segmentation• Number of exclusions less in FIRST segmentations• Note that not always the same subjects get excluded
(but great overlap ±70%)
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Putamen segmentation (1)
FIRST (good) FreeSurfer 5.3 (bad)
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Putamen segmentation (2)
FIRST (bad blue) FreeSurfer 5.3 (good blue)
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Pallidum segmentation (1)
FIRST (good) FreeSurfer 5.3 (bad)
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Pallidum segmentation (2)
FIRST (blue bad) FreeSurfer 5.3 (blue ok)
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Poor segmentations child MRI scans Input from ENIGMA PI’s (Thompson’s group,
meeting Feb 25, 2015 in Amsterdam)? Input from ADHD and autism working group
(meeting February 25, 2015)? Additional ideas?
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Current status per sitePlease, check whether the information is
correct and let us know whether the planning (see slide 47) is feasible for your site.
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Arnold (CAN) Memory of understanding (still waiting for
the properly checked MOU!!) Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status running recon-all please, proceed a.s.a.p.!
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Benedetti (ITA) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Beucke (DEU) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status quality checking data
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Cheng (CHN) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status recon-all VUmc is waiting for remaining data (must be uploaded) to be preprocessed at VUmc Amsterdam (NLD)
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Denys (NLD) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Fitzgerald (USA) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status quality checking data
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Gruner (USA) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status quality checking data
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van den Heuvel (NLD) Memory of understanding Putamen/pallidum images Histograms + Summarystats (1.5T data) R statistical output (1.5T data)
Current Status FINISHED subcortical analyses 1.5T data R statistical analyses 3.0T data
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Hoexter (BRA) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status checking outliers on histograms
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Huyser (NLD)Analyses performed by van den Heuvel (NLD)
Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Koch (DEU) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Kwon (KOR) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status quality checking data
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Lazaro (ESP) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status preparing for R analyses
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Mataix-Cols (SWE)Analyses performed by van den Heuvel (NLD)
Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status recon-all (we are solving issues with converting hdr format files)
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Menchon (ESP) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status quality checking data
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Nakamae (JPN) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Nakao (JPN) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status recon-all please, proceed a.s.a.p.!
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Reddy (IND) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status quality checking
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Rosenberg (USA)Analyses performed by Fitzgerald/Hanna (USA)
Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status agreement with Wayne State University for data transfer
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Simpson (USA) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Soreni (USA) Memory of understanding (still waiting for
properly checked MOU!!) Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status running recon-all please, proceed a.s.a.p.!
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Spalletta (ITA) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Stein (ZAF) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Tolin (USA) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status checking histograms
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Walitza (CHE) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Wang (CHN) Memory of understanding Putamen/pallidum images Histograms + Summarystats R statistical output
Current Status FINISHED subcortical analyses
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Memory of Understanding Arnold Soreni
Benedetti Huyser Reddy Beucke Koch
Rosenberg Cheng Kwon Simpson Denys Lazaro Spalletta Fitzgerald Mataix-Cols Stein Gruner Menchon Tolin van den Heuvel Nakamae Walitza Hoexter Nakao Wang
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Have sent putamen/pallidum images
Arnold Mataix-Cols Rosenberg Cheng Nakao Soreni Hoexter
Benedetti Koch Simpson Beucke Kwon Spalletta Denys Lazaro Stein Fitzgerald Menchon Tolin Gruner Nakamae Walitza Huyser Reddy Wang van den Heuvel
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First instructionsHistograms & Summarystats
Arnold Hoexter Reddy Beucke Kwon Rosenberg Cheng Mataix-Cols Soreni Fitzgerald Menchon Tolin Gruner Nakao
Finished: Benedetti Koch Spalletta Denys Lazaro Stein Huyser Nakamae Walitza van den Heuvel Simpson Wang
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Second instructionsR statistical analyses Arnold Hoexter Nakao Beucke Kwon Reddy Cheng Lazaro Rosenberg Fitzgerald Mataix-Cols Soreni Gruner Menchon Tolin
Finished: Benedetti Koch Spalletta Denys Nakamae Stein van den Heuvel Simpson Walitza Huyser Spalletta Wang
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Planning meta-analyses for the subcortical volumes Decision on the putamen / pallidum segmentations
> February 25, 2015 Solution for segmentation pediatric MRIs
> March 2015 All sites finished all steps for the subcortical analyses (in FS 5.3),
including analyses in R > March 31, 2015
Meta-analyses (van den Heuvel / Boedhoe at VUmc) > April 2015
Discussion on results during TC, May 28, 2015 Draft paper
> May/June 2015
Feasible?If so, let’s try to meet these deadlines!
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses
is dependent on progress subcortical analyses, but to be started a.s.a.p. (at least for the sites that already finished the subcortical analyses).
1. draft form analysis plans, for additional subcortical meta-analyses
2. preparation mega-analyses on pooled raw data3. expert-subgroups for specific topics/analyses4. funding5. status GWAS6. future meetings
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses3. draft form analysis plans, for additional (sub)cortical meta-
analyses1. See attachment (used in other ENIGMA working groups): comments?2. Forwarded initial ideasNB. A separate analyses plan form will be drafted for the mega-analyses
(on pooled raw data)
4. preparation mega-analyses on pooled raw data5. expert-subgroups for specific topics/analyses6. funding7. status GWAS8. future meetings
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Analysis plans - meta-analyses van den Heuvel / Boedhoe
General OCD-control comparison subcortical General OCD-control comparison cortical
(but also possible that another site leads this analyses plan)
....sorry, I received some initial ideas from members, but I can’t find the emails now (between the thousands of ENIGMA-OCD-emails in my box)
... Please fill in the analyses plan form and forward this to me. I will make a list of the ideas and forward it to all members for comments and approval.
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses3. draft form analysis plans, for additional subcortical meta-
analyses4. preparation mega-analyses on pooled raw data
1. Participants2. Ethical approval3. Formation shared database (MRI + phenotype)4. Analyses plans
5. expert-subgroups for specific topics/analyses6. funding7. status GWAS8. future meetings
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Pooling raw data for mega-analysis Advantages:
1 group (or more groups in parallel on different analyses plans) can work on the data processing, QC, analyses, and re-analyses without bothering all sides.
Excellent opportunities for specific analyses on clinical phenotype, age effects, co-morbidity, medication effects, etc.
Great opportunity to replicate (+ improve) the OBIC mega-analysis (Am J Psychiatry 2014)
But: We first have to construct the database (based on the
OBIC experience, this is a lot of work (!), and we have to solve data transfer issues, etc.)
Before we can start with analyses on shared database, the data must be checked, cleaned, etc.
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Raw data sharing for mega-analysis (1)Site Yes No Maybe
Arnold
Benedetti
Beucke
Cheng
Denys
Fitzgerald
Gruner
van den Heuvel
Hoexter
Huyser
Koch
Kwon
Lazaro
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Raw data sharing for mega-analysis (2)Site Yes No Maybe
Mataix-Cols
Menchon
Nakamae
Nakao
Reddy ?
Rosenberg
Simpson
Soreni
Spalletta
Stein
Tolin
Walitza
Wang
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses3. draft form analysis plans, for additional subcortical meta-
analyses4. preparation mega-analyses on pooled raw data5. expert-subgroups for specific topics/analyses
E.g. rs fMRI, DTI, child OCD, imaging-geneticsPlease, email me about your wishes to take initiative to one of these topics!
6. funding7. status GWAS8. future meetings
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses3. draft form analysis plans, for additional subcortical meta-
analyses4. preparation mega-analyses on pooled raw data5. expert-subgroups for specific topics/analyses6. Funding
1. Awarded: NIH grant Paul Thompson2. Not awarded: ERC (Horizon2020) Odile van den Heuvel3. Submitted/pending: Carles Soriano-Mas4. Plans/options: ?
7. status GWAS8. future meetings
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses3. draft form analysis plans, for additional
subcortical meta-analyses4. preparation mega-analyses on pooled raw data5. expert-subgroups for specific topics/analyses6. funding7. status GWAS: Carol/Jim, what’s the status?8. future meetings
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Agenda1. status subcortical meta-analyses2. planning cortical meta-analyses3. draft form analysis plans, for additional subcortical meta-analyses4. preparation mega-analyses on pooled raw data5. expert-subgroups for specific topics/analyses6. funding7. status GWAS8
8. future meetings1. ENIGMA working group PI’s
- Feb 25: Thompson et al. (UCS) + Dutch PI’s/members (MDD, OCD, autism, ADHD, addiction working groups)
- June 2015: ENIGMA working group PI’s meeting, prior to HBM, Hawaii
2. ENIGMA OCD working group members- SOBP/APA 2015, Toronto, May 14-16 (SOBP), 16-20 (APA)- HBM 2015, Hawaii, June 14-18Please, email me to inform me about your conference plans, so that I can plan
an informal meeting these conferences.