Commit f118c7ec authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
Browse files

fix typos

parent e1afe68d
...@@ -40,7 +40,7 @@ or message on Open WIN Slack #data-sharing-decision-tree ...@@ -40,7 +40,7 @@ or message on Open WIN Slack #data-sharing-decision-tree
4. Christoph Arthofer/ he/his / WIN/FMRIB / [@cart](https://git.fmrib.ox.ac.uk/cart) / 0000-0003-1474-9963 4. Christoph Arthofer/ he/his / WIN/FMRIB / [@cart](https://git.fmrib.ox.ac.uk/cart) / 0000-0003-1474-9963
5. Mats van Es/ he/his/ WIN-OHBA / [@psych1435](https://git.fmrib.ox.ac.uk/psyc1435) 5. Mats van Es/ he/his/ WIN-OHBA / [@psych1435](https://git.fmrib.ox.ac.uk/psyc1435)
6. Marieke Martens / she/her / Psychiatry / [@mmartens](https://git.fmrib.ox.ac.uk/mmartens) / https://orcid.org/0000-0003-0108-1327 6. Marieke Martens / she/her / Psychiatry / [@mmartens](https://git.fmrib.ox.ac.uk/mmartens) / https://orcid.org/0000-0003-0108-1327
7. 7.
## Participation Guidelines ## Participation Guidelines
- We value the participation of every member of our community and want to ensure that every contributor has an enjoyable and fulfilling experience. Please show respect and courtesy to other community members at all times. - We value the participation of every member of our community and want to ensure that every contributor has an enjoyable and fulfilling experience. Please show respect and courtesy to other community members at all times.
...@@ -51,7 +51,7 @@ or message on Open WIN Slack #data-sharing-decision-tree ...@@ -51,7 +51,7 @@ or message on Open WIN Slack #data-sharing-decision-tree
**Imagine you are a WIN researcher asking "*Can I share my data?*", or "*How can I share my data?*"** **Imagine you are a WIN researcher asking "*Can I share my data?*", or "*How can I share my data?*"**
- -
The "decision tree" document and appendices should guide you through the necessary stages to prepare your data for sharing. The "decision tree" document and appendices should guide you through the necessary stages to prepare your data for sharing.
...@@ -87,39 +87,39 @@ Add below any comments about each of the steps in this process. ...@@ -87,39 +87,39 @@ Add below any comments about each of the steps in this process.
##### Date of birth ##### 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 - 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 - When sharing data with industry recently, industry partner was happy to keep year of birth only
- Radiographers really lilke to keep full date of birth. - Radiographers really like to keep full date of birth.
- Sharing dicoms or nifti? P1vital wanted the dicoms. - 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 ##### 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 - Same with size and weight. +1
##### Time and date ##### 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 ##### 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 ##### 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 #### 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 - 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. - usually get defaced images with the skull.
- skull gives a bit of reference (SIENA) - 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. - non-skull stripped images for olfactory bulb segmentation.
#### Quality control #### Quality control
- Mriqc can be run on XNAT. Would you run mriqc before your own analysis anyway? - Mriqc can be run on XNAT. Would you run mriqc before your own analysis anyway?
- mriqc still being used - mriqc still being used
- usually done manually/visally. - usually done manually/visually.
- People would be happy to run a simple qc as a recomended step - People would be happy to run a simple qc as a recommended step
- biobank by default extrqacts some qc measures (qc IDPs) but it doesn't exclude. - biobank by default extracts some qc measures (qc IDPs) but it doesn't exclude.
- **Talk to Fidel about the biobank pipeline** - **Talk to Fidel about the biobank pipeline**
...@@ -131,7 +131,7 @@ Add below any comments about each of the steps in this process. ...@@ -131,7 +131,7 @@ Add below any comments about each of the steps in this process.
#### electrophys #### electrophys
- **We don't know much about electrophys metadata...*** - **We don't know much about electrophys metadata...***
- Ususally you have MRI as well - Usually you have MRI as well
- head circumference, height, weight - head circumference, height, weight
- which things are recorded as standard (e.g. dental wire is important to know) - which things are recorded as standard (e.g. dental wire is important to know)
...@@ -142,21 +142,21 @@ Add below any comments about each of the steps in this process. ...@@ -142,21 +142,21 @@ Add below any comments about each of the steps in this process.
- dcm2niix is maybe comparable with the BIDS .json. - dcm2niix is maybe comparable with the BIDS .json.
- downloaded data from the magnet also comes with a .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. - 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) - 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)
#### Experimental protocol #### Experimental protocol
- Usually share the experimental script (e.g. in psychtoolbox, psychopy), along with a brief description in a README file. - 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. - 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 - 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 - 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 - Study design section
- wouldn't have anything specific to the participant, but it would have the different tests, questionnaires etc. - 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. - Exclusion criteria might also be useful, but not in this section.
- **How would we make sure useful things about blinding, counterbalancing etc is communicted** - **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. 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 ...@@ -193,7 +193,7 @@ Mats: People that are accessing the data have to agree they won't try to de-anon
#### Approval of access #### Approval of access
- ORCID? Insitutional email? - ORCID? Institutional email?
- Log of who accesses the images - Log of who accesses the images
- password provided by us and renewed frequently (request from an ethics team for covid study ?OCMR) - 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). - 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).
...@@ -215,14 +215,14 @@ Mats: People that are accessing the data have to agree they won't try to de-anon ...@@ -215,14 +215,14 @@ Mats: People that are accessing the data have to agree they won't try to de-anon
#### What worked? #### What worked?
- Having an open conversation - Having an open conversation
- Good sized group for open discussion - Good sized group for open discussion
- Having different perspectives from different kind of researchers was very useful - Having different perspectives from different kind of researchers was very useful
- Quick way of gathering information we all have in our head but which is not directly out there to find online for example - Quick way of gathering information we all have in our head but which is not directly out there to find online for example
#### What didn't work? #### What didn't work?
- comment here - comment here
#### What would you change? #### What would you change?
- Some info on what we were going to talk about in the meeting would have been helpful to know beforehand. - Some info on what we were going to talk about in the meeting would have been helpful to know beforehand.
#### What surprised you? #### What surprised you?
- comment here - comment here
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