Validation of BIDS2NDA output

[mtnhuck]

Hi,
I ran bids2nda without any issues and it generated a image03.txt. This is the same dataset that passed the bids validator I mentioned in a previous issue. I ran the NDA Validator and Upload tool, which ran but provides quite a few errors, all specifically related to missing data in fields for non-DICOM images.

As best as I can tell the

fields missing data (left) map onto the following json fields (right):
photomet_interpret PhotometricInterpretation
experiment_id ProcedureStepDescription
image_orientation ImageOrientationPatient
scanner_software_versions_pd SoftwareVersions
image_slice_thickness SliceThickness -> This one seem to be present in some of the .json files and not others (present for all functional/anatomical/fmap phasediff runs but not for fmap magnitude. I'm assuming the last part may be a bug on the conversion to BIDS but image_slice_thickness doesn't seem to map onto SliceThickness from the json file for any of the files.

Couldn't find these in the json files (or not exactly sure what they

are looking for):
extent5_type
image_unit5
image_extent5
image_resolution5

Would there be a way to potentially pull data formats directly from NDA as mentioned in #8?

Thanks in advance and please let me know if I can provide more information etc.
Jeremy

[chrisgorgo]

Those fields seems to be added more recently, thus breaking the converter. Pulling a never version of image03.txt would help testing, but work needs to be done to implement new mapings from BIDS to NDA (for the new fileds). Would you like to help implementing those? Best, Chris

…

On Thu, Jan 11, 2018 at 3:30 PM, mtnhuck ***@***.***> wrote: Hi, I ran bids2nda without any issues and it generated a image03.txt. This is the same dataset that passed the bids validator I mentioned in a previous issue. I ran the NDA Validator and Upload tool, which ran but provides quite a few errors, all specifically related to missing data in fields for non-DICOM images. As best as I can tell the fields missing data (left) map onto the following json fields (right): *photomet_interpret PhotometricInterpretation experiment_id ProcedureStepDescription image_orientation ImageOrientationPatient scanner_software_versions_pd SoftwareVersions* *image_slice_thickness SliceThickness* -> This one seem to be present in some of the .json files and not others (present for all functional/anatomical/fmap phasediff runs but not for fmap magnitude. I'm assuming the last part may be a bug on the conversion to BIDS but image_slice_thickness doesn't seem to map onto SliceThickness from the json file for any of the files. Couldn't find these in the json files (or not exactly sure what they are looking for): *extent5_type image_unit5 image_extent5 image_resolution5* Would there be a way to potentially pull data formats directly from NDA as mentioned in #8 <#8>? Thanks in advance and please let me know if I can provide more information etc. Jeremy — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp3jDOoYV8DZe24GL4rz05SPlgdRsks5tJpmPgaJpZM4Rbmzs> .

[mtnhuck]

Of course, I’m happy to help however I can. Just let me know what I can do to move things in the right direction. Cheers Jeremy On Thu, Jan 11, 2018 at 8:02 PM Chris Filo Gorgolewski < notifications@github.com> wrote:

…

Those fields seems to be added more recently, thus breaking the converter. Pulling a never version of image03.txt would help testing, but work needs to be done to implement new mapings from BIDS to NDA (for the new fileds). Would you like to help implementing those? Best, Chris On Thu, Jan 11, 2018 at 3:30 PM, mtnhuck ***@***.***> wrote: > Hi, > I ran bids2nda without any issues and it generated a image03.txt. This is > the same dataset that passed the bids validator I mentioned in a previous > issue. I ran the NDA Validator and Upload tool, which ran but provides > quite a few errors, all specifically related to missing data in fields for > non-DICOM images. > As best as I can tell the > > fields missing data (left) map onto the following json fields (right): > > > > *photomet_interpret PhotometricInterpretation experiment_id > ProcedureStepDescription image_orientation ImageOrientationPatient > scanner_software_versions_pd SoftwareVersions* > *image_slice_thickness SliceThickness* -> This one seem to be present in > some of the .json files and not others (present for all > functional/anatomical/fmap phasediff runs but not for fmap magnitude. I'm > assuming the last part may be a bug on the conversion to BIDS but > image_slice_thickness doesn't seem to map onto SliceThickness from the json > file for any of the files. > Couldn't find these in the json files (or not exactly sure what they > > are looking for): > > > > *extent5_type image_unit5 image_extent5 image_resolution5* > > Would there be a way to potentially pull data formats directly from NDA as > mentioned in #8 <#8>? > > Thanks in advance and please let me know if I can provide more information > etc. > Jeremy > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#11>, or mute the thread > < https://github.com/notifications/unsubscribe-auth/AAOkp3jDOoYV8DZe24GL4rz05SPlgdRsks5tJpmPgaJpZM4Rbmzs > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGhtiN6TuG7hmNmqTqSss3BhDA4w2EJUks5tJq8jgaJpZM4Rbmzs> .

[chrisgorgo]

If you could send a Pull Request on GitHub with modifications adding at least some of the missing mappings that would be greatly appreciated. Best, Chris

…

On Jan 11, 2018 9:18 PM, "mtnhuck" ***@***.***> wrote: Of course, I’m happy to help however I can. Just let me know what I can do to move things in the right direction. Cheers Jeremy On Thu, Jan 11, 2018 at 8:02 PM Chris Filo Gorgolewski < ***@***.***> wrote: > Those fields seems to be added more recently, thus breaking the converter. > Pulling a never version of image03.txt would help testing, but work needs > to be done to implement new mapings from BIDS to NDA (for the new fileds). > Would you like to help implementing those? > > Best, > Chris > > On Thu, Jan 11, 2018 at 3:30 PM, mtnhuck ***@***.***> wrote: > > > Hi, > > I ran bids2nda without any issues and it generated a image03.txt. This is > > the same dataset that passed the bids validator I mentioned in a previous > > issue. I ran the NDA Validator and Upload tool, which ran but provides > > quite a few errors, all specifically related to missing data in fields > for > > non-DICOM images. > > As best as I can tell the > > > > fields missing data (left) map onto the following json fields (right): > > > > > > > > *photomet_interpret PhotometricInterpretation experiment_id > > ProcedureStepDescription image_orientation ImageOrientationPatient > > scanner_software_versions_pd SoftwareVersions* > > *image_slice_thickness SliceThickness* -> This one seem to be present in > > some of the .json files and not others (present for all > > functional/anatomical/fmap phasediff runs but not for fmap magnitude. I'm > > assuming the last part may be a bug on the conversion to BIDS but > > image_slice_thickness doesn't seem to map onto SliceThickness from the > json > > file for any of the files. > > Couldn't find these in the json files (or not exactly sure what they > > > > are looking for): > > > > > > > > *extent5_type image_unit5 image_extent5 image_resolution5* > > > > Would there be a way to potentially pull data formats directly from NDA > as > > mentioned in #8 <#8>? > > > > Thanks in advance and please let me know if I can provide more > information > > etc. > > Jeremy > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub > > <#11>, or mute the thread > > < > https://github.com/notifications/unsubscribe-auth/ AAOkp3jDOoYV8DZe24GL4rz05SPlgdRsks5tJpmPgaJpZM4Rbmzs > > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#11 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ AGhtiN6TuG7hmNmqTqSss3BhDA4w2EJUks5tJq8jgaJpZM4Rbmzs> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp7O00v7V_73MgWI2uBzIyXEdG8xyks5tJusfgaJpZM4Rbmzs> .

[agrethe]

Hello,

Just following up on this to see if there are plans to update bids2nda to be compliant with the image03 format? I have the same issues with missing data for the above fields, as well as fields that are optional for image03.csv but generate warnings with the NDA validator tool because the columns don't exist.

Thank you --
Amanda