SIG Meeting Monday 11am at Open Science Room

Pradeep Reddy Raamana

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Jun 6, 2019, 5:25:34 AM6/6/19

to NIQC

Hi Everyone,

The SIG meeting will be on Monday (June 10th) at 11am in the Open Science Room (refer to OHBM maps of the venue).

Agenda for the meeting:

Meet and greet (first 20-30 mins)
Short presentation on niQC goals, progress so far, and future plans
Open discussion towards achieving niQC goals

See you all there! And bring your friends.

Feel free to suggest other ideas for the agenda.

Thanks,

Pradeep

--

Postdoctoral fellow

Neuroinformatics,

Rotman Research Institute,

Baycrest Health Sciences.

3560 Bathurst Street, Toronto, ON
Canada, M6A 2E1.
Phone: +1 416-785-2500 x6408.

Uludag, Kamil

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Jun 6, 2019, 5:44:17 AM6/6/19

to Pradeep Reddy Raamana, NIQC

Good luck. Sorry that I cannot be there. Cheers, Kamil!

Get Outlook for Android

From: ni...@googlegroups.com <ni...@googlegroups.com> on behalf of Pradeep Reddy Raamana <praa...@research.baycrest.org>
Sent: Thursday, June 6, 2019 5:25:21 AM
To: NIQC
Subject: [niQC] SIG Meeting Monday 11am at Open Science Room

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Greg Operto

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Jun 7, 2019, 5:59:03 AM6/7/19

to niQC

Dear Pradeep,

Thanks for organizing it.

Depending on how many we are, maybe the 'Meet and greet' part could include a round table introduction to know about individual implications in QC across the group? Or we are too many?

Looking forward to my first SIG meeting with you all.

Kind regards,

Greg

Fidel Alfaro Almagro

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Jun 7, 2019, 7:12:34 AM6/7/19

to Greg Operto, niQC

Hi,

Would it be possible to include the events organised in the SIG to the OHBM app? I do not think it is possible to add events to our personal schedules if that event is not in the app.

Cheers.

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Pradeep Reddy Raamana

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Jun 7, 2019, 7:33:52 AM6/7/19

to Fidel Alfaro Almagro, Greg Operto, niQC

Hi All,

I sent you a calendar invite to make it easy to add this to your calendar.

Here is the calendar you can subscribe to, to future participation really easy. Keep an eye out for tutorial modality-experts or tool makers etc, that we hope to run periodically after the conference:

https://calendar.google.com/calendar?cid=cmVzZWFyY2guYmF5Y3Jlc3Qub3JnX2JycWMxMjloaWZkaHFmanFnN3VtY3RwN2pzQGdyb3VwLmNhbGVuZGFyLmdvb2dsZS5jb20

Thanks,

Pradeep

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Pradeep Reddy Raamana

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Jun 7, 2019, 7:35:57 AM6/7/19

to Fidel Alfaro Almagro, Greg Operto, niQC

Greg, Yes, I envision Meet & Greet to be a round table intro, and we might improvise the format if the attendance is too large.

Pradeep Reddy Raamana

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Jun 7, 2019, 8:04:10 AM6/7/19

to Fidel Alfaro Almagro, Greg Operto, niQC

Sorry for too many emails - just want to clarify original date on the calendar invite was wrong (was today), but the event is modified to be on the coming Monday. If you are able to and planning to attend, you can add it to calendar. Thanks.

Henk-Jan Mutsaerts

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Jun 10, 2019, 5:43:26 AM6/10/19

to Pradeep Reddy Raamana, niQC

Dear Pradeep,

Also there seemed to be an option to join through video call with GoogleMeet, but this doesn't seem to work..

I used the link in the calendar invite!

Cheers, Henk

Best wishes/hartelijke groet,

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

To view this discussion on the web visit https://groups.google.com/d/msgid/niqc/CAKYYBvoPfVPdAGAG4zYfcdbFddwKQnKeAXxyRETiacMVtM6e_w%40mail.gmail.com.

rcwe...@gmail.com

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Jun 10, 2019, 6:24:50 AM6/10/19

to Henk-Jan Mutsaerts, Pradeep Reddy Raamana, niQC

To follow up, and to ensure others are not alienated/excluded by choosing to analyze their data with SPM, perhaps a good coding practice would be that any QC tools (working w image data) expose an API that is BIDS-compliant, but that can also support a bare API that would allow for expansion to beyond BIDS, such as the derivatives people spoke of, or BIDS2 etc., or other formats (SPM).

Robert Welsh
Assoc Prof

Dept Psychiatry

University of Utah

------------------------------

typos due to iPhone 4S

To view this discussion on the web visit https://groups.google.com/d/msgid/niqc/CAPO0dgoqTXbkokqMVt_MU2JEK40UQEXxy2idDVLjKsMz_A0CyQ%40mail.gmail.com.

Henk-Jan Mutsaerts

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Jun 10, 2019, 6:55:49 AM6/10/19

to rcwe...@gmail.com, Pradeep Reddy Raamana, niQC

I would agree. But eventually SPM will use BIDS as well, is my understanding.

We are currently porting PyBIDS to Matlab for ExploreASL, for these reasons.

Best wishes/hartelijke groet,

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

Liew, Sook-Lei

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Jun 10, 2019, 9:23:37 AM6/10/19

to Pradeep Reddy Raamana, niQC, anishak...@gmail.com

Thanks again for organizing us Pradeep!

I just wanted to follow up on Bob's comment about making QC processes easy and fun, and share a little about Anisha Keshavan and my experiences with this, which might be helpful for others.

My lab has to QC hundreds of stroke lesion masks, which is really boring and painful. Anisha helped us build Braindrles (https://braindrles.us), a fun web-based app for stroke lesion QC where you swipe right or left on stroke lesions.

Some lessons we learned in the process - (1) making QC into a game with points, levels to unlock, and a leaderboard makes it more engaging, (2) the QC'd image should be presented in a simple/intuitive format, and should make a complex problem simple (e.g., we switched from static pictures of lesion masks to triplanar blinking gifs to make it an easier and faster decision), and (3) there should be adequate user training on what is good versus bad (i.e., we provide a tutorial, and then in the first few levels, a random subset of images have ground truth labels that give feedback on if you're right or wrong).

We actually made braindrles at the OHBM hackathon last year, but ended up revising a lot of elements to make it more attractive so people would use it. We just re-released it today and would welcome any feedback (and help getting the word out: https://twitter.com/NPNLatUSC/status/1138040659204616193).

Also, if anyone else is interested in using this platform for their own QC projects, Anisha has now built her initial app braindr (https://braindr.us/#/) into this really nice SwipesforScience platform (https://swipesforscience.org/) so she can help others develop for their own QC apps - contact her (anishak...@gmail.com) if interested!

Cheers,
Lei

--
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Assistant Professor
Director, Neural Plasticity and Neurorehabilitation Laboratory
Chan Division of Occupational Science and Occupational Therapy,
Biokinesiology and Physical Therapy, Biomedical Engineering, and Neurology
USC Stevens Neuroimaging and Informatics Institute
University of Southern California
Email: sl...@usc.edu | Web: http://npnl.usc.edu

________________________________________
From: ni...@googlegroups.com <ni...@googlegroups.com> on behalf of Henk-Jan Mutsaerts <henkjanm...@gmail.com>
Sent: Monday, June 10, 2019 3:55:36 AM
To: rcwe...@gmail.com
Cc: Pradeep Reddy Raamana; niQC
Subject: Re: [niQC] Re: SIG Meeting Monday 11am at Open Science Room

I would agree. But eventually SPM will use BIDS as well, is my understanding.
We are currently porting PyBIDS to Matlab for ExploreASL, for these reasons.

Best wishes/hartelijke groet,

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

On Mon, 10 Jun 2019 at 12:24, <rcwe...@gmail.com<mailto:rcwe...@gmail.com>> wrote:
To follow up, and to ensure others are not alienated/excluded by choosing to analyze their data with SPM, perhaps a good coding practice would be that any QC tools (working w image data) expose an API that is BIDS-compliant, but that can also support a bare API that would allow for expansion to beyond BIDS, such as the derivatives people spoke of, or BIDS2 etc., or other formats (SPM).

Robert Welsh
Assoc Prof
Dept Psychiatry
University of Utah
------------------------------
typos due to iPhone 4S

On Jun 10, 2019, at 11:43, Henk-Jan Mutsaerts <henkjanm...@gmail.com<mailto:henkjanm...@gmail.com>> wrote:

Dear Pradeep,

Also there seemed to be an option to join through video call with GoogleMeet, but this doesn't seem to work..
I used the link in the calendar invite!

Cheers, Henk

Best wishes/hartelijke groet,

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

On Fri, 7 Jun 2019 at 14:04, Pradeep Reddy Raamana <praa...@research.baycrest.org<mailto:praa...@research.baycrest.org>> wrote:
Sorry for too many emails - just want to clarify original date on the calendar invite was wrong (was today), but the event is modified to be on the coming Monday. If you are able to and planning to attend, you can add it to calendar. Thanks.

On Fri, Jun 7, 2019 at 1:35 PM Pradeep Reddy Raamana <praa...@research.baycrest.org<mailto:praa...@research.baycrest.org>> wrote:
Greg, Yes, I envision Meet & Greet to be a round table intro, and we might improvise the format if the attendance is too large.

On Fri, Jun 7, 2019 at 1:33 PM Pradeep Reddy Raamana <praa...@research.baycrest.org<mailto:praa...@research.baycrest.org>> wrote:
Hi All,

I sent you a calendar invite to make it easy to add this to your calendar.

Here is the calendar you can subscribe to, to future participation really easy. Keep an eye out for tutorial modality-experts or tool makers etc, that we hope to run periodically after the conference:

https://calendar.google.com/calendar?cid=cmVzZWFyY2guYmF5Y3Jlc3Qub3JnX2JycWMxMjloaWZkaHFmanFnN3VtY3RwN2pzQGdyb3VwLmNhbGVuZGFyLmdvb2dsZS5jb20<https://urldefense.proofpoint.com/v2/url?u=https-3A__calendar.google.com_calendar-3Fcid-3DcmVzZWFyY2guYmF5Y3Jlc3Qub3JnX2JycWMxMjloaWZkaHFmanFnN3VtY3RwN2pzQGdyb3VwLmNhbGVuZGFyLmdvb2dsZS5jb20&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=T5tk-FGsu_rsab-Xlv9K2Fy2R1MECdheKZ2BhKyJ4DA&m=SAblih80AWDbhn6MAxxLMAY3cb-AO1lFiiRjmNO5hyc&s=81nLVD1NRx53LLgMmlkSQB7mDSYqtVA6a46c2bx22JQ&e=>

Thanks,
Pradeep

On Fri, Jun 7, 2019 at 1:12 PM Fidel Alfaro Almagro <fidel.alfa...@gmail.com<mailto:fidel.alfa...@gmail.com>> wrote:
Hi,

Would it be possible to include the events organised in the SIG to the OHBM app? I do not think it is possible to add events to our personal schedules if that event is not in the app.

Cheers.

On Fri, 7 Jun 2019, 10:59 Greg Operto, <gop...@barcelonabeta.org<mailto:gop...@barcelonabeta.org>> wrote:
Dear Pradeep,

Thanks for organizing it.
Depending on how many we are, maybe the 'Meet and greet' part could include a round table introduction to know about individual implications in QC across the group? Or we are too many?
Looking forward to my first SIG meeting with you all.

Kind regards,
Greg

On Thursday, June 6, 2019 at 11:25:34 AM UTC+2, Pradeep Reddy Raamana wrote:
Hi Everyone,

The SIG meeting will be on Monday (June 10th) at 11am in the Open Science Room (refer to OHBM maps of the venue).

Agenda for the meeting:

* Meet and greet (first 20-30 mins)
* Short presentation on niQC goals, progress so far, and future plans
* Open discussion towards achieving niQC goals

See you all there! And bring your friends.

Feel free to suggest other ideas for the agenda.

Thanks,
Pradeep

--
Postdoctoral fellow

Neuroinformatics<https://urldefense.proofpoint.com/v2/url?u=http-3A__research.baycrest.org_sstrother&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=T5tk-FGsu_rsab-Xlv9K2Fy2R1MECdheKZ2BhKyJ4DA&m=SAblih80AWDbhn6MAxxLMAY3cb-AO1lFiiRjmNO5hyc&s=aIysg90Vo7ojcOSssIiPpjSIWhwSs9k33wRG6kJkwN4&e=>,
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3560 Bathurst Street, Toronto, ON
Canada, M6A 2E1.
Phone: +1 416-785-2500 x6408.

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3560 Bathurst Street, Toronto, ON
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Phone: +1 416-785-2500 x6408.

--
Postdoctoral fellow

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Postdoctoral fellow

Neuroinformatics<https://urldefense.proofpoint.com/v2/url?u=http-3A__research.baycrest.org_sstrother&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=T5tk-FGsu_rsab-Xlv9K2Fy2R1MECdheKZ2BhKyJ4DA&m=SAblih80AWDbhn6MAxxLMAY3cb-AO1lFiiRjmNO5hyc&s=aIysg90Vo7ojcOSssIiPpjSIWhwSs9k33wRG6kJkwN4&e=>,
Rotman Research Institute<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.baycrest.org_research_rotman-2Dresearch-2Dinstitute_&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=T5tk-FGsu_rsab-Xlv9K2Fy2R1MECdheKZ2BhKyJ4DA&m=SAblih80AWDbhn6MAxxLMAY3cb-AO1lFiiRjmNO5hyc&s=8pTlP-hk0Z9YUa07eMap2k2jClm3qC39IrvcXrcBPYQ&e=>,
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3560 Bathurst Street, Toronto, ON
Canada, M6A 2E1.
Phone: +1 416-785-2500 x6408.

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Henk-Jan Mutsaerts

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Jun 10, 2019, 9:55:48 AM6/10/19

to Liew, Sook-Lei, Pradeep Reddy Raamana, niQC, anishak...@gmail.com

Yes, I think this is a great initiative, Anisha and me had a Skype before to see if we can use this amongst others for ASL MRI.

I'm actually thinking of writing a European/Dutch grant for standardising QC, perhaps we can have a Skype to combine forces?

Henk

Best wishes/hartelijke groet,

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

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JB Poline

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Jun 10, 2019, 7:38:38 PM6/10/19

to Henk-Jan Mutsaerts, Liew, Sook-Lei, Pradeep Reddy Raamana, niQC, anishak...@gmail.com

Hi all,

Sorry I had to miss the meeting - but this sounds a great initiative. I think INCF might help you with the grant - and certainly to organize meetings.

cheers

JB

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Vince Calhoun

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Jun 11, 2019, 1:01:52 AM6/11/19

to jbpo...@gmail.com, Henk-Jan Mutsaerts, Liew, Sook-Lei, Pradeep Reddy Raamana, niQC, anishak...@gmail.com

Agreed! Sorry I had to miss as well, too much running around for me at this OHBM!

Vince

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Henk-Jan Mutsaerts

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Jun 11, 2019, 3:20:57 AM6/11/19

to JB Poline, Liew, Sook-Lei, Pradeep Reddy Raamana, niQC, anishak...@gmail.com

Thanks, that sounds great, I will come back on it soon!

Henk

Best wishes/hartelijke groet,

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

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Jean Chen

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Jun 11, 2019, 9:44:08 AM6/11/19

to Henk-Jan Mutsaerts, JB Poline, Liew, Sook-Lei, Pradeep Reddy Raamana, niQC, anishak...@gmail.com

I’m also sorry for missing this SIG meeting — had intended to attend but was feeling unwell Monday morning. Will catch up with you at Baycrest Pradeep.

Jean

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