[BIDS] Don't assume task name about broccoli

[wanderine]

Yes, how can I extract the study name from the json file? Should I get
"Name" from dataset_description.json and then get "TaskName" from
task-${Name}_bold.json ?

For the rhyme judgment dataset, "Name" is "Rhyme judgment" and not
"rhymejudgment"

2016-08-31 20:18 GMT+02:00 Chris Filo Gorgolewski [email protected]
:

Currently the task name is hardcoded as rhymejudgement. It would be
better to iterate over all tasks for each subject:

https://github.com/wanderine/BROCCOLI/blob/master/code/
bids/broccolipipeline.sh#L137

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Anders Eklund, PhD

[wanderine]

Sorry, is there a file that contains all task names?

2016-08-31 20:33 GMT+02:00 Anders Eklund [email protected]:

Yes, how can I extract the study name from the json file? Should I get
"Name" from dataset_description.json and then get "TaskName" from
task-${Name}_bold.json ?

For the rhyme judgment dataset, "Name" is "Rhyme judgment" and not
"rhymejudgment"

2016-08-31 20:18 GMT+02:00 Chris Filo Gorgolewski <
[email protected]>:

Currently the task name is hardcoded as rhymejudgement. It would be
better to iterate over all tasks for each subject:

https://github.com/wanderine/BROCCOLI/blob/master/code/bids/
broccolipipeline.sh#L137

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Anders Eklund, PhD

Anders Eklund, PhD

[chrisgorgo]

The most reliable and quickest way to get task labels is to get them from the file names themselves. This bash command will get you all of the task labels for a dataset in the current working directory:

find . -name "*_bold.nii*" | grep -oP "task-([a-zA-Z0-9]+)" | cut -d "-" -f 2 | uniq

However in your case I would recommend refactoring the analyze_subject function to take three files:

1. skullstripped T1w (you would do it onece per subject not once per _bold file as you are doing now)
2. _bold.nii* file
3. _events.tsv file

This way you can iterate over subjects, find T1w (if there are more than one grab the first one for now) perform skullstripping, find all _bold.nii* files and for each one find the corresponding _events.tsv and call the analyze_subject.

[wanderine]

Would it make sense to put all task names (and the number of runs per task)
in the main json file?

2016-08-31 22:30 GMT+02:00 Chris Filo Gorgolewski [email protected]
:

The most reliable and quickest way to get task labels is to get them from
the file names themselves. This bash command will get you all of the task
labels for a dataset in the current working directory:

find . -name "_bold.nii" | grep -oP "task-([a-zA-Z0-9]+)" | cut -d "-"
-f 2 | uniq

However in your case I would recommend refactoring the analyze_subject
function to take three files:

1. skullstripped T1w (you would do it onece per subject not once per _bold
   file as you are doing now)
2. _bold.nii* file
3. _events.tsv file

This way you can iterate over subjects, find T1w (if there are more than
one grab the first one for now) perform skullstripping, find all _bold.nii*
files and for each one find the corresponding _events.tsv and call the
analyze_subject.

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Anders Eklund, PhD

[chrisgorgo]

It's technically possible, but it would provide a redundant piece of information and (most importantly) making this new field compulsory would break backwards compatibility rendering already distributed BIDS dataset invalid.

Did the command I sent you not work?

[wanderine]

It works, but the task names seems like such important information that it
should be included in the main json file...

2016-09-06 16:30 GMT+02:00 Chris Filo Gorgolewski [email protected]
:

It's technically possible, but it would provide a redundant piece of
information and (most importantly) making this new field compulsory would
break backwards compatibility rendering already distributed BIDS dataset
invalid.

Did the command I sent you not work?

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Anders Eklund, PhD