[Loris-dev] question regarding MRI uploader

[Ling Ma]

Hi Ioannis,

I try to answer your question without checking in detail. My memory might
not be accurate.

1). GUI imaging uploader is just a tool that helps you to upload a zip file
without actually processing it. So when it is stuck with "in progress",
then this uploading task could be considered dead, you can just open the
page to start over again. Of course you could remove the record. Since this
is only a tool helping you upload images, this tool won't read the DICOM
information, it just read the file name to process.
2). As I remember, the MRI type in the file name won't be taken into
consideration, instead I suppose the DICOM information should be used, I
could check later for details.
3). if you just upload an image, it failed without having been processed,
you can just remove the record from "mri_upload" table or just start over
again, you can remove the corresponding file if you wish to free up the
used space. Of course you should be careful in doing so.

I feel that you are not using image processing tool up to right now, the
imaging uploader is not all, the uploading doesn't do all the work as you
assume, The purpose of the "Imaging Uploader" is "The imaging uploader is
intended to allow users to upload, browse, and track pipeline insertion
progress." (source:
https://github.com/aces/Loris/tree/master/modules/imaging_uploader/README.md
)

Instead the real work is done by imaging processing package Loris-MRI (
https://github.com/aces/Loris-MRI).

If the files have been processed but without being successful, under the
image uploading processing tool package Loris-MRI, (
https://github.com/aces/Loris-MRI), there is a folder called "tools", there
is a delete_imaging_upload.pl, which could be used to easily remove any
unsuccessful imaging loading.

Hope this could help you out.

Best regards,
Ling Ma

On Wed, Mar 4, 2020 at 8:03 PM Ioannis Pappas <ioannis at berkeley.edu> wrote:

> Hi loris dev team
> I have a question about uploading some of the data.
>
> For now I am experimenting with the GUI and I uploaded a .zip folder
> containing some BOLD for one participant. However, I am getting an error
> message saying that it cannot read the PatientName field in one of the
> dicoms. However that dicom header field exists (itself is a struct
> containing a field named FamilyName with the name of the patient). Now the
> bar is stuck and it says "in progress". What is your advice on this?
>
> 2. I am still confused as to how each uploaded dicom zip will be assigned
> to each mri type via the mri_protocol table. For example if I upload the
> pscid_candid_V1_BOLD_resting_MtzVA_8.zip file that corresponds to my BOLD
> data, is the regex expression in the mri_protocol the one that I will need
> to modify in order to assign my mri_scan_type of bold to that particular
> upload?
>
> 3. What is the easiest way to remove patients and their associated data?
> For example now my data is stuck "in progress" and I would like to get rid
> of it.
>
> Thank you very much in advance.
> Best wishes,
> Ioannis
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