Commit f118c7ec authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
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fix typos

parent e1afe68d
......@@ -87,39 +87,39 @@ Add below any comments about each of the steps in this process.
##### Date of birth
- People wouldn't routinely go back to the dicom to get DOB (or year), unless you have acquired the data from someone else. Useful sanity check. +1
- When sharing data with inducstry recently, industry partner was happy to keep year of birth only
- Radiographers really lilke to keep full date of birth.
- When sharing data with industry recently, industry partner was happy to keep year of birth only
- Radiographers really like to keep full date of birth.
- Sharing dicoms or nifti? P1vital wanted the dicoms.
- **table position is used in biobank pipeline (coordinatre in the scanner)**. Used in an IDP.
- **table position is used in biobank pipeline (coordinate in the scanner)**. Used in an IDP.
##### Patient sex
- You would expect this to be someonwhere else, but good for sanity check. +1
- You would expect this to be somewhere else, but good for sanity check. +1
- Same with size and weight. +1
##### Time and date
- acquistion time can be used to control for arousal. I would not put this in a normal database of metadata, but it is something we might come back to with a secondary hypothesis.
- acquisition time can be used to control for arousal. I would not put this in a normal database of metadata, but it is something we might come back to with a secondary hypothesis.
##### Which scanner
- Device serial number and insitutional address. Multi centre covid study use this information...! Biobank pipeline contrains a call to the pipeline to find out the address...!
- Device serial number and institutional address. Multi centre covid study use this information...! Biobank pipeline contains a call to the pipeline to find out the address...!
##### Study description
- One instance with a participant which was scanned over different projects and combineed to make a new one.
- One instance with a participant which was scanned over different projects and combined to make a new one.
#### Defacing and skull stripping
- The face is usually critical for coregistration. What would be the advice; sharing the defaced structural + the coregistration info (that was derived from the complete structural)? +100. Note this is a unique
- usually get defaced images with the skull.
- skull gives a bit of reference (SIENA)
- Non-skull stripped images are used to create a referfence space for creating them oxford template [Oxford-MM-1](https://git.fmrib.ox.ac.uk/cart/oxford-mm-templates); MMORF can be used to register non-skull stripped images to this template
- Non-skull stripped images are used to create a reference space for creating them oxford template [Oxford-MM-1](https://git.fmrib.ox.ac.uk/cart/oxford-mm-templates); MMORF can be used to register non-skull stripped images to this template
- non-skull stripped images for olfactory bulb segmentation.
#### Quality control
- Mriqc can be run on XNAT. Would you run mriqc before your own analysis anyway?
- mriqc still being used
- usually done manually/visally.
- People would be happy to run a simple qc as a recomended step
- biobank by default extrqacts some qc measures (qc IDPs) but it doesn't exclude.
- usually done manually/visually.
- People would be happy to run a simple qc as a recommended step
- biobank by default extracts some qc measures (qc IDPs) but it doesn't exclude.
- **Talk to Fidel about the biobank pipeline**
......@@ -131,7 +131,7 @@ Add below any comments about each of the steps in this process.
#### electrophys
- **We don't know much about electrophys metadata...***
- Ususally you have MRI as well
- Usually you have MRI as well
- head circumference, height, weight
- which things are recorded as standard (e.g. dental wire is important to know)
......@@ -142,7 +142,7 @@ Add below any comments about each of the steps in this process.
- dcm2niix is maybe comparable with the BIDS .json.
- downloaded data from the magnet also comes with a .json
- what is in the non-BIDS .json which comes with a normally downloaded form the magnet nii.
- don't forget about the acquisition database. Could recommend that you share the entire acquistion protocol. **think about de-identifying the acquisition reports**
- don't forget about the acquisition database. Could recommend that you share the entire acquisition protocol. **think about de-identifying the acquisition reports**
- make sure all the radiographers positioning etc info is included (the radiographers protocol). Is this generated by default? If yes, the radiographers should upload (if no privacy concerns)
......@@ -150,13 +150,13 @@ Add below any comments about each of the steps in this process.
#### Experimental protocol
- Usually share the experimental script (e.g. in psychtoolbox, psychopy), along with a brief description in a README file.
- What about more detailed stuff about the session design. Some information might be on the trial registry.
- Could share a SOP for the testing, if you have that, but not everyone would ahve that.
- Could share a SOP for the testing, if you have that, but not everyone would have that.
- In the paper you would describe briefly
- More detail would be in the ethics. Could share the **study design section**. Don't need to share the whole docuemtn as this has other info (e.g. recriutment, resaearchers names).
- More detail would be in the ethics. Could share the **study design section**. Don't need to share the whole document as this has other info (e.g. recruitment, researchers names).
- protocols.io. really good for wetlab experiments (has fields for doses etc.)... Not sure if it is well suited to our standard studies
- Study design section
- wouldn't have anything specific to the participant, but it would have the different tests, questionnaires etc.
- might also have things in there that you wouldn;t want to share.
- might also have things in there that you wouldn't want to share.
- Exclusion criteria might also be useful, but not in this section.
- **How would we make sure useful things about blinding, counterbalancing etc is communicted**
Mats: In my experience , most often a file is shared (e.g. .mat file), containing some subject specific information, including counterbalancing, amounts of sessions completed etc.
......@@ -193,7 +193,7 @@ Mats: People that are accessing the data have to agree they won't try to de-anon
#### Approval of access
- ORCID? Insitutional email?
- ORCID? Institutional email?
- Log of who accesses the images
- password provided by us and renewed frequently (request from an ethics team for covid study ?OCMR)
- BHC requests (and DPUK) have to submit a request to access the data. The more things you ask for, the more you have to review (then need a review committee).
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