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

[Ling Ma]

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.
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>
>>
>>
>>
> _______________________________________________
> 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/20200330/5ad908b3/attachment.html>