From AMORALESPINZON at BWH.HARVARD.EDU Mon Aug 8 17:02:38 2022 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 8 Aug 2022 21:02:38 +0000 Subject: [Loris-dev] Issue uploading segmentations Message-ID: <265195DF-323E-4FAB-A08A-4EAC7F6FD193@bwh.harvard.edu> Dear LorisDev team, I am uploading segmentations to images already uploaded into LORIS using the script "register_processed_data.pl". I have used this script before but now I'm getting the following errors: === Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112. Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112. Attribute (db) does not pass the type constraint because: Validation failed for 'NeuroDB::Database' with value 0 (not isa NeuroDB::Database) at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Moose/Object.pm line 24 Moose::Object::new('NeuroDB::objectBroker::MriScannerOB', 'db', 0) called at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 961 NeuroDB::MRI::findScannerID(undef, undef, undef, undef, 0, 'REF(0x3ca3fc0)', 0, 'NeuroDB::Database=HASH(0x3d7c8b0)') called at /anom_project/bin/mri/uploadNeuroDB/register_processed_data.pl line 266 Argument "8Exiting now\n\n" isn't numeric in right bitshift (>>) at /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310. Argument "\nAn error occurred when running register_processed_data..." isn't numeric in right bitshift (>>) at /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310. 0fileLikeName:%710881_m00_t1c% === This is command line I'm executing: === register_processed_data.pl -profile prod -sourcePipeline T2Vol -tool T2Vol -pipelineDate 2022-08-08 -coordinateSpace ISPC-t2w -outputType ct2f -inputFileIDs 571801 -sourceFileID 571801 -scanType ct2f -file /anom_project/file.mnc.gz === I am using v23.0 of Loris-MRI and LORIS v23.0.2. Any ideas on how can I solve this issue? Do I have to upgrade Loris-MRI? Best 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. From cecile.madjar at mcin.ca Tue Aug 9 09:07:50 2022 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 9 Aug 2022 09:07:50 -0400 Subject: [Loris-dev] Issue uploading segmentations In-Reply-To: <265195DF-323E-4FAB-A08A-4EAC7F6FD193@bwh.harvard.edu> References: <265195DF-323E-4FAB-A08A-4EAC7F6FD193@bwh.harvard.edu> Message-ID: Hi Alfredo, Looking at the code of LORIS-MRI 23.0, I do not see why the $db variable is not passed correctly to the function NeuroDB::MRI::findScannerID. The line numbers in your log and the ones in the code seem to be different. Has there been any code changes made? What are the variables passed to the NeuroDB::MRI::findScannerID function call in register_processed_data.pl and the variables expected by the function NeuroDB/MRI.pm findScannerID? There might be some discrepancies there? Best, C?cile On Mon, Aug 8, 2022 at 5:03 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > I am uploading segmentations to images already uploaded into LORIS using > the script "register_processed_data.pl". I have used this script before > but now I'm getting the following errors: > > === > Use of uninitialized value $patientName in pattern match (m//) at > /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112. > Use of uninitialized value $patientName in pattern match (m//) at > /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112. > Attribute (db) does not pass the type constraint because: Validation > failed for 'NeuroDB::Database' with value 0 (not isa NeuroDB::Database) at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Moose/Object.pm line 24 > Moose::Object::new('NeuroDB::objectBroker::MriScannerOB', 'db', 0) > called at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 961 > NeuroDB::MRI::findScannerID(undef, undef, undef, undef, 0, > 'REF(0x3ca3fc0)', 0, 'NeuroDB::Database=HASH(0x3d7c8b0)') called at > /anom_project/bin/mri/uploadNeuroDB/register_processed_data.pl line 266 > Argument "8Exiting now\n\n" isn't numeric in right bitshift (>>) at > /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310. > Argument "\nAn error occurred when running register_processed_data..." > isn't numeric in right bitshift (>>) at > /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310. > 0fileLikeName:%710881_m00_t1c% > === > > This is command line I'm executing: > === > register_processed_data.pl -profile prod -sourcePipeline T2Vol -tool > T2Vol -pipelineDate 2022-08-08 -coordinateSpace ISPC-t2w -outputType > ct2f -inputFileIDs 571801 -sourceFileID 571801 -scanType ct2f -file > /anom_project/file.mnc.gz > === > > I am using v23.0 of Loris-MRI and LORIS v23.0.2. > > Any ideas on how can I solve this issue? Do I have to upgrade Loris-MRI? > > Best 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 Mass General > Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline < > https://www.massgeneralbrigham.org/complianceline> . > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted 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: From AMORALESPINZON at BWH.HARVARD.EDU Mon Aug 15 13:21:47 2022 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 15 Aug 2022 17:21:47 +0000 Subject: [Loris-dev] Issue uploading segmentations In-Reply-To: <265195DF-323E-4FAB-A08A-4EAC7F6FD193@bwh.harvard.edu> References: <265195DF-323E-4FAB-A08A-4EAC7F6FD193@bwh.harvard.edu> Message-ID: <57693648-149F-4108-A552-41F0BAE17342@bwh.harvard.edu> Hi C?cile, I have indeed a different version from v23.0. This is the version of the MRI.pm I?m using right now: https://github.com/SPINEProject/Loris-MRI/blob/master/uploadNeuroDB/NeuroDB/MRI.pm I believe I used this after a fix you wrote. As you pointed out the inputs for the function findScannerID in the file MRI.pm has changed as I don?t have the parameter $register_new which is why the $db is zero: https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/register_processed_data.pl#L264 https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/NeuroDB/MRI.pm#L938 I will upgrade my code to the v23.0-release and test. I?ll keep you posted. Best, Alfredo. On Aug 8, 2022, at 5:02 PM, Morales Pinzon, Alfredo > wrote: External Email - Use Caution Dear LorisDev team, I am uploading segmentations to images already uploaded into LORIS using the script "register_processed_data.pl". I have used this script before but now I'm getting the following errors: === Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112. Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112. Attribute (db) does not pass the type constraint because: Validation failed for 'NeuroDB::Database' with value 0 (not isa NeuroDB::Database) at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Moose/Object.pm line 24 Moose::Object::new('NeuroDB::objectBroker::MriScannerOB', 'db', 0) called at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 961 NeuroDB::MRI::findScannerID(undef, undef, undef, undef, 0, 'REF(0x3ca3fc0)', 0, 'NeuroDB::Database=HASH(0x3d7c8b0)') called at /anom_project/bin/mri/uploadNeuroDB/register_processed_data.pl line 266 Argument "8Exiting now\n\n" isn't numeric in right bitshift (>>) at /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310. Argument "\nAn error occurred when running register_processed_data..." isn't numeric in right bitshift (>>) at /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310. 0fileLikeName:%710881_m00_t1c% === This is command line I'm executing: === register_processed_data.pl -profile prod -sourcePipeline T2Vol -tool T2Vol -pipelineDate 2022-08-08 -coordinateSpace ISPC-t2w -outputType ct2f -inputFileIDs 571801 -sourceFileID 571801 -scanType ct2f -file /anom_project/file.mnc.gz === I am using v23.0 of Loris-MRI and LORIS v23.0.2. Any ideas on how can I solve this issue? Do I have to upgrade Loris-MRI? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. 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Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://secure-web.cisco.com/1EXLcGfORQAU8J_0p-Luc-Ta71zLwOwiyeeWg04DlORafYE3CSSrG4ZZv-bJVlTBKD9Droe23LCgIPzkttkbwD-d5FwIlXTyaJxmlV22YtiqQ3IIqv9_ZCtASSw-5Vvp3-yRgN2DQ6v6Ij_gMiHdPvVMfRJrZHTN85-fRWb9PfDXZLbg_d3Dw0sCl6BNtnoiv1kCf60mJqrJmo1TPJkAPR45IN9bAcXqgFkBv5__Wm7EGqgm3qJgUEyM8oqLQfp5xwD1zFPJy0YUUpz-336qgWhpnwXQxlK0_MKmjI9v8XbW_TQvEQ9aKHHicBDnnn7KajnTmUpH7I40YyRxRlRjZoA/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev The information in this e-mail is intended only for the person to whom it is addressed. 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URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Aug 22 16:31:48 2022 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 22 Aug 2022 20:31:48 +0000 Subject: [Loris-dev] Issue: same hash for different files Message-ID: <542C054E-66E7-4E40-A32A-4CAE302E6BE8@bwh.harvard.edu> Dear LorisDev team, I just came across an issue for about 100 segmentations that I?m attaching to some images using the script ?register_processed_data.pl?. I found that the hash for two different files is exactly the same, and thus one of the files cannot be uploaded. The segmentations are different and are linked to two different images. Here is the code that is finding the ?duplicate? hash in the database: https://github.com/SPINEProject/Loris-MRI/blob/62ae20930af73935a3a03071307b2575abf165f1/uploadNeuroDB/NeuroDB/MRI.pm#L1188-L1206 What do you think I can do in this case? I?m happy to share the anonymized segmentation files if needed. I am running Loris-MRI v23.0-release. On a side note, when the script ? register_processed_data.pl? exits there is no error message send to the terminal. Can we add an error printer when this happens? This is where the script is exiting in my case: https://github.com/SPINEProject/Loris-MRI/blob/62ae20930af73935a3a03071307b2575abf165f1/uploadNeuroDB/register_processed_data.pl#L329 Best 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Mon Aug 22 17:25:00 2022 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 22 Aug 2022 17:25:00 -0400 Subject: [Loris-dev] Issue: same hash for different files In-Reply-To: <542C054E-66E7-4E40-A32A-4CAE302E6BE8@bwh.harvard.edu> References: <542C054E-66E7-4E40-A32A-4CAE302E6BE8@bwh.harvard.edu> Message-ID: Hi Alfredo, Actually, the function that computes the md5hash is in https://github.com/SPINEProject/Loris-MRI/blob/62ae20930af73935a3a03071307b2575abf165f1/uploadNeuroDB/NeuroDB/MRI.pm#L1135 . My guess is that the list of headers used to determine the uniqueness of the file is not enough to differentiate between the two segmentation files you mention even though they are from two completely different images. Maybe you need to add another header in that function to make sure that each segmentation file you insert is unique? I don't know what those files look like but I would investigate in that direction if I were you. Hope this helps, C?cile On Mon, Aug 22, 2022 at 4:32 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > I just came across an issue for about 100 segmentations that I?m attaching > to some images using the script ?register_processed_data.pl?. I found > that the hash for two different files is exactly the same, and thus one of > the files cannot be uploaded. The segmentations are different and are > linked to two different images. > > Here is the code that is finding the ?duplicate? hash in the database: > > https://github.com/SPINEProject/Loris-MRI/blob/62ae20930af73935a3a03071307b2575abf165f1/uploadNeuroDB/NeuroDB/MRI.pm#L1188-L1206 > > What do you think I can do in this case? I?m happy to share the anonymized > segmentation files if needed. > > I am running Loris-MRI v23.0-release. > > On a side note, when the script ? register_processed_data.pl? exits there > is no error message send to the terminal. Can we add an error printer > when this happens? This is where the script is exiting in my case: > > https://github.com/SPINEProject/Loris-MRI/blob/62ae20930af73935a3a03071307b2575abf165f1/uploadNeuroDB/register_processed_data.pl#L329 > > Best 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 Mass General > Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline . > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted 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: