[Loris-dev] LORIS ~ 2.500 errors uploading

[Nicolas Brossard]

Hi Alfredo,

Sorry for the late reply. I'll be able to address this tomorrow. I'll keep
in touch.


Best,
Nicolas


On Mon, Jan 25, 2021 at 3:14 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Nicolas,
>
> I am following up on this issue. I can share some dicom files through the
> loris sftp if needed.
>
> Best,
> Alfredo.
>
> On Jan 14, 2021, at 2:33 PM, Morales Pinzon, Alfredo <
> AMORALESPINZON at BWH.HARVARD.EDU> wrote:
>
> Hi Nicolas,
>
> We uploaded another study in LORIS with 7.554 visits. Out of those visits,
> 825 don't have any images uploaded and 1.700 have missing images. I am
> checking the log files but most of the time they don’t have an ERROR or
> WARNING message which makes finding issues very time consuming .
>
> So far these are my findings:
>
> For the 825 visit where no images were uploaded this is what I can see in
> the logs:
>
> Error Cases
> 'inserting into the database: 0' 350
> 'Visit label does not exist’ (Issues on Alfredo’s side) 265
> 'inserting into the database: 0' & 'Visit label does not exist'  12
> patient-name doesn\'t match 99
> The \'PatientName\' DICOM field cannot be extracted 19
> You can\'t use it with data from multiple studies 23
> Dicom to Minc conversion failed 10
> Log not created 1
> Unknown 46
>
> For the 350 cases where the logs say 'inserting into the database: 0’ I
> have found so far the following messages:
>
> - No data could be converted into valid MINC files.
> - The candidate info validation has failed.
>
> I check 5 cases with the instructions you provided in a previous email and
> all the conversion to dcm2minc worked. I reran 2 of those cases, and
> the log files suggested to run the following command (with different
> parameters for each case):
>
> ===
> \/data_\/ipmsa\/loris_data\/IPMSA\/bin\/mri/uploadNeuroDB/tarchiveLoader.pl
> -globLocation -profile prod
> \/data_\/ipmsa\/loris_data\/IPMSA\/data\/tarchive\/DCM_2014\-02\-04_ImagingUpload\-22\-30\-pKguhD\.tar
> -uploadID 44052 -verbose
> ===
>
> After the execution the images were properly uploaded for one case and
> the other one is missing a flair image.
>
>
> For the 1.700 that have missing images I have been looking at some log
> files but I haven’t found warnings or errors, as happened previously with
> the missing t1c in a previous study.
>
> What do you suggest to help me go through all these cases? We can start
> working with some examples and figure out what is happening and how can we
> fixed.
>
> Based on this current situation, I strongly suggest to improve the error
> and warning logging in the uploading process for LORIS.
>
> Best,
> Alfredo.
>
>
>
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