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nottingham-neuroimaging / qa

qa - quality assurance 7T fMRI data
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build up a set of QA related functions / code for fMRI data #1

Closed schluppeck closed 4 years ago

schluppeck commented 9 years ago

points to think about for QA:

Sue mentioned that it would be a good idea to keep track of data quality in all of our fMRI scans, which will help to detect problems early. This would involve:

We should also consider looking at some already existing tools. At NYU - just because I know about it - they have developed a set of tools that we could make use of? http://cbi.nyu.edu/software/dataQuality.php

ppzstf commented 9 years ago

I guess I was saying use the data we collect as our own tSNR check, which is what we are now doing for some studied and we should spread across group, rather than collect extra data. QA is now being done on phantom, etc.. but as load is different it doesn't pick up all possible issues. So we don't want to reinvent this set-up, instead our own data sets serve as assessment of this stability. We have some code and should discuss on Tuesday. I think only minor tweaks needed I don't think we need to reinvent anything or need anything exhaustive, it's pretty clear when it fails and tSNR drops. There are also measures from each scan day we should log and just sign off that all PO passed. Let's keep it simple but fail safe and not make it too much extra work. Catch up next week. Sue

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On 24 Sep 2015, at 18:06, Denis Schluppeck notifications@github.com<mailto:notifications@github.com> wrote:

points to think about for QA:

Sue mentioned that it would be a good idea to keep track of data quality in all of our fMRI scans, which will help to detect problems early. This would involve:

before we reinvent the wheel:

We should also consider looking at some already existing tools. At NYU - just because I know about it - they have developed a set of tools that we could make use of? http://cbi.nyu.edu/software/dataQuality.php

— Reply to this email directly or view it on GitHubhttps://github.com/nottingham-neuroimaging/qa/issues/1.

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panchuelo commented 9 years ago

I think there is code in the MR centre to do the QA already, I will ask Kath. Rosa

On 24/09/2015 18:06, Denis Schluppeck wrote:

points to think about for QA:

Sue mentioned that it would be a good idea to keep track of data quality in all of our fMRI scans, which will help to detect problems early. This would involve:

* tagging on one/two simple / quick scans to each scanning session
  that would allow us to track SNR / temporal SNR and other bits
  of the data
* running those data through some matlab code / FSL code wrapped
  in an appropriate script and storing info somewhere: centrally
  hosted CSV file? MAT file?
* producing a minimal report that we can easily look
      o *what*: tSNR maps? tSNR values for a small ROI?
      o *where/how*: simple set of files that you can look at with
        a web-browser? Matlab |publish()| or even just some
        hand-rolled basic /markdown/ / /html/ could do the trick.

before we reinvent the wheel:

We should also consider looking at some already existing tools. At NYU

— Reply to this email directly or view it on GitHub https://github.com/nottingham-neuroimaging/qa/issues/1.

Rosa Maria Sanchez Panchuelo Post-doctoral Research fellow Sir Peter Mansfield Magnetic Resonance Centre University of Nottingham University Park Nottingham, NG7 2RD United Kingdom +44 115 84 66003

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schluppeck commented 9 years ago

... had a brief chat with AP. The "proper" QA is in hand and will be very complete across sites. I explained that we just want to have a mini-set of internal consistency checks for each of our data sets and he thought it was a good idea.

I managed to get a copy of the PSIR code that runs on the console and had a brief look. Most of it looks like it's about getting the right info out of XML files.

Might be worth creating "issues" for different bits of this and seeing how we can tackle them one by one.