[Loris-dev] question regarding MRI uploader

[Cecile Madjar]

Hi Ioannis,

I would also recommend reading the documentation in the LORIS-MRI repo here
<https://github.com/aces/Loris-MRI/tree/master/docs> to get a better
understanding on how the insertion pipelines work.

Re-2) the protocol identification is performed based on the scan's TR, TE,
TI, slice thickness parameters read from the image (see section 2.2.1 of
this page
<https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md#221-database>
with
explanation of the mri_scan_type, mri_protocol and mri_protocol_checks
tables).

Hope this helps,

Cécile

On Wed, Mar 4, 2020 at 10:57 PM Ling Ma <lingyun.ma at mcin.ca> wrote:

> 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
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20200305/0c83e6ac/attachment-0001.html>