[Loris-dev] [IPMSA] Remove MRI files from a project

Mon Mar 30 22:28:49 EDT 2020

Hi Alfredo,

Have you source that environment file? Or you can logout then login to try
to activate that file.

What you need is:
PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:/data/%PROJECT%/bin/mri/dicom-archive:$PERL5LIB.
So I suppose that my suggested method should work for you, if not, try to
check PERL5LIB with "echo $PERL5LIB"

Good luck.

Ling Ma

On Mon, Mar 30, 2020 at 10:18 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Ling Ma,
>
> Thank you for the prompt response.
>
> I already had the statement because I am upgrading from v18.0.0. However I
> double checked and the .bashrc file has the statement.
>
> Any other ideas of where to look for?
>
> Regards,
> Alfredo.
>
> On Mar 30, 2020, at 9:49 PM, Ling Ma <lingyun.ma at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> I believe you need to read the
> https://github.com/aces/Loris-MRI/blob/21.0-dev/README.md#5-configure-paths-and-environment,
> which says:
>
> "Ensure that /home/lorisadmin/.bashrc includes the statement:
>
> source /data/$projectname/bin/mri/environment
>
> Then source the .bashrc file."
>
> Regards,
>
> Ling Ma
>
> On Mon, Mar 30, 2020 at 8:08 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi Cécile and LorisDev team,
>>
>> Indeed, there are some breaking changes so I decided to upgrade to
>> LORIS-MRI v21.0.0. After upgrading I am running the suggested script “
>> cleanup_paths_of_violation_tables.pl” before running the deletion script
>> but I get the following error:
>>
>> ===
>> *bin/mri/tools*$ perl cleanup_paths_of_violation_tables.pl
>> Can't locate DICOM/DICOM.pm in @INC (you may need to install the
>> DICOM::DICOM module) (@INC contains: /opt/minc/1.9.16/perl
>> /opt/minc/1.9.16/pipeline
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl
>> /opt/minc/1.9.16/pipeline
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /opt/minc/1.9.16/perl
>> /opt/minc/1.9.16/pipeline
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB /etc/perl
>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1
>> /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5
>> /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47.
>> BEGIN failed--compilation aborted at
>> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 47.
>> Compilation failed in require at cleanup_paths_of_violation_tables.pl
>> line 9.
>> BEGIN failed--compilation aborted at cleanup_paths_of_violation_tables.pl
>> line 9.
>> ===
>>
>> Any idea how to solve it? I couldn’t find it in the troubleshooting
>> guideline (
>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/AppendixA-Troubleshooting_guideline.md
>> )
>>
>> Regards,
>> Alfredo.
>>
>> On Mar 9, 2020, at 11:17 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Alfredo,
>>
>> Have you tested your MRI code since you did the upgrade on the LORIS?
>> There might be some SQL changes impacting the LORIS-MRI side as well
>> (conversion of the ranges in mri_protocol and mri_protocol_checks to MIN
>> and MAX columns for example).
>>
>> If all works well, you can try downloading and testing the
>> delete_imaging_upload.pl and it may work as is.
>>
>> Let me know how this goes!
>>
>> Cécile
>>
>> On Mon, Mar 9, 2020 at 9:12 AM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Dear Loris DevTeam,
>>>
>>> I finally upgraded LORIS to v21.0.0 so that we can delete images using
>>> the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to
>>> v21.0.0, I am currently running v18.0.0.
>>>
>>> Given that I have made modification to the core of the library (MRI.pm)
>>> and created scripts for uploading masks and transformation that are working
>>> properly and might be impacted if I upgrade the code, would it be possible
>>> to “import” and use the script delete_imaging_upload.pl without
>>> upgrading LORIS-MRI?
>>>
>>> Let me know if this is possible. I would prefer to keep the library as
>>> it is cause it’s working perfect for us right now.
>>>
>>> Regards,
>>> Alfredo.
>>>
>>> On Mar 2, 2020, at 12:02 PM, Morales Pinzon, Alfredo <
>>> AMORALESPINZON at BWH.HARVARD.EDU> wrote:
>>>
>>> Hi Cécile,
>>>
>>> I finally upgraded LORIS to v21.0.0 so that we can delete images using
>>> the scripts from LORIS-MRI. Next step would be to upgrade LORIS-MRI to
>>> v21.0.0, I am currently running v18.0.0.
>>>
>>> Given that I have made modification to the core of the library (MRI.pm)
>>> and created scripts for uploading masks and transformation that are working
>>> properly and might be impacted if I upgrade the code, would it be
>>> possible to “import” and use the script delete_imaging_upload.pl without
>>> upgrading LORIS-MRI?
>>>
>>> Let me know if this is possible. I would prefer to keep the library as
>>> it is cause it’s working perfect for us right now.
>>>
>>> Regards,
>>> Alfredo.
>>>
>>> On Feb 4, 2020, at 11:26 AM, Morales Pinzon, Alfredo <
>>> AMORALESPINZON at BWH.HARVARD.EDU> wrote:
>>>
>>> Hi Cécile,
>>>
>>> Thank you for your answer. I will use it once some uploading processes
>>> are finished so that I can upgrade LORIS to the its last version where the
>>> script is available. I will tell you how it goes.
>>>
>>> Best,
>>> Alfredo.
>>>
>>> On Feb 4, 2020, at 9:46 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Hi Alfredo,
>>>
>>> Indeed, the delete_imaging_upload.pl script was designed to properly
>>> remove imaging dataset without touching the other tables in the database.
>>> By defaults, the script will create a backup of the removed dataset
>>> (files + MySQL entries) which is always nice to have in case the delete
>>> script was run on a wrong dataset.
>>>
>>> Run "delete_imaging_upload.pl -h " to see the list of options that can
>>> be used.
>>>
>>> Let me know if you have any questions.
>>>
>>> Cécile
>>>
>>> On Mon, Feb 3, 2020 at 6:37 PM Morales Pinzon, Alfredo <
>>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>>
>>>> Hi Cecile,
>>>>
>>>> In IPMSA we need to re-upload a whole study in terms of MRI images.
>>>> Given that I already created all the centers, users in centers, candidates,
>>>> and visits (clinical and mri), would it be possible to only remove the MRI
>>>> images previously uploaded? Looking at the script
>>>> delete_imaging_upload.pl
>>>> <https://github.com/aces/Loris-MRI/blob/9fe2972c15e4ddb5da0914d751f9bdb74bf2d7f8/tools/delete_imaging_upload.pl> it
>>>> seems to be possible (I can get all the Tarchive IDs assoicated) but I want
>>>> to confirm before I move forward. Please let me know if this is possible.
>>>>
>>>> Thank you for all your help.
>>>>
>>>> Regards,
>>>> Alfredo.
>>>>
>>>>
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>>>
>>>
>>>
>>>
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