From AMORALESPINZON at bwh.harvard.edu Mon Apr 8 18:01:22 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 8 Apr 2019 22:01:22 +0000 Subject: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. Message-ID: Dear LoriDev team, Out of 82 MRI sessions that I was uploading into LORIS, 15 could not be uploaded due to the following error: --------------------------------------- Running now the following command: /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 20844 /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz -verbose /AAA/loris_data/IPMSA/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-9-29-1gMub2 /AAA/loris_data/BBB/data/tarchive -clobber -database -profile prod -verbose Source: /tmp/ImagingUpload-9-29-1gMub2 Target: /AAA/loris_data/BBB/data/tarchive Testing for database connectivity. Database is available. The target directory does not contain a single DICOM file. The dicomtar execution has failed --------------------------------------- I checked the file /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz and it has dicom files in it. Is there something a need to double check? Best regards, Alfredo. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Apr 8 18:36:50 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 8 Apr 2019 22:36:50 +0000 Subject: [Loris-dev] [IPMSA] Error: DBD::mysql::st execute failed: Incorrect date value: '' for column 'DateAcquired' Message-ID: Dear LorisDev team, I have 2 MRI sessions that could not be uploaded due to the following error: -------------------------- Use of uninitialized value $_ in pattern match (m//) at /AAA/loris_data/IPMSA/bin/mri//batch_uploads_imageuploader line 92. DBD::mysql::st execute failed: Incorrect date value: '' for column 'DateAcquired' at row 1 at /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 238. DBD::mysql::st execute failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` (`TarchiveID`) ON DELETE CASCADE) at /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. DBD::mysql::st execute failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` (`TarchiveID`) ON DELETE CASCADE) at /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. -------------------------- This is what I get in the log file: /AAA/ANOM/CCC//log_batch_imageuploader_AAA10292_850501_w048.txt -------------------------- Running now the following command: /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 20872 /AAA/ANOM/CCC//AAA10292_850501_w048.tar.gz -verbose /AAA/loris_data/BBB/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-12-4-kG9b0L /AAA/loris_data/BBB/data/tarchive -clobber -database -profile prod -verbose Source: /tmp/ImagingUpload-12-4-kG9b0L Target: /AAA/loris_data/BBB/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-12-4-kG9b0L You are creating a tar with the following command: tar -cf /AAA/loris_data/BBB/data/tarchive/ImagingUpload-12-4-kG9b0L.tar ImagingUpload-12-4-kG9b0L getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-12-4-kG9b0L * Archive target location : /AAA/loris_data/BBB/tarchive/DCM__ImagingUpload-12-4-kG9b0L.tar * Name of creating host : 132.216.133.49 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-04-07 12:05:46 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 19fbaf1fcab253c3bdf741f4b7b5d4a2 ImagingUpload-12-4-kG9b0L.tar * md5sum for DICOM tarball gzipped : 3611bbab463663880c58fe32def90c8a ImagingUpload-12-4-kG9b0L.tar.gz * md5sum for complete archive : 2dc51a007126ad41e8e0195eda37a378 DCM__ImagingUpload-12-4-kG9b0L.tar Adding archive info into database Failed running query: INSERT INTO tarchive SET DicomArchiveID = ?, PatientName = ?, PatientID = ?, PatientDoB = ?, PatientGender = ?, DateAcquired = ?, ScannerManufacturer = ?, ScannerModel = ?, ScannerSerialNumber = ?, ScannerSoftwareVersion = ?, CenterName = ?, AcquisitionCount = ?, NonDicomFileCount = ?, DicomFileCount = ?, CreatingUser = ?, SourceLocation = ?, sumTypeVersion = ?, AcquisitionMetadata = ?, DateLastArchived = NOW() , tarTypeVersion = ?, md5sumArchive = ?, md5sumDicomOnly = ?, ArchiveLocation = ?, CreateInfo = ? , DateFirstArchived = NOW(), neurodbCenterName = ? Removing temporary files from target location The database command failed The dicomtar execution has failed -------------------------- This cases were part of a list of 82 cases where 65 were correctly uploaded (15 had another type of error that I just reported in a different email). I can review the files with somebody from your team if required. Best regards, Alfredo. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Apr 9 10:05:26 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 9 Apr 2019 10:05:26 -0400 Subject: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. In-Reply-To: References: Message-ID: Hi Alfredo, I have a feeling you are encountering an issue that was fixed in release 20.2 of LORIS-MRI where DICOM files without the header (0020,0032) were automatically rejected by the script get_dicom_info.pl with the error message saying that the file is not a DICOM, while it is actually a DICOM... If you don't wish to upgrade your LORIS instance to 20.2 right away, you can take a look at the following PR that solved the issue: https://github.com/aces/Loris-MRI/pull/365 to implement the fix. Hope this helps! Let me know how it goes, C?cile On Mon, Apr 8, 2019 at 6:02 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LoriDev team, > > Out of 82 MRI sessions that I was uploading into LORIS, 15 could not be > uploaded due to the following error: > > --------------------------------------- > Running now the following command: > /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile > prod -upload_id 20844 /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz > -verbose > > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/dicomTar.pl > /tmp/ImagingUpload-9-29-1gMub2 /AAA/loris_data/BBB/data/tarchive -clobber > -database -profile prod -verbose > Source: /tmp/ImagingUpload-9-29-1gMub2 > Target: /AAA/loris_data/BBB/data/tarchive > > Testing for database connectivity. > Database is available. > > The target directory does not contain a single DICOM file. > > The dicomtar execution has failed > --------------------------------------- > > I checked the file /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz and > it has dicom files in it. Is there something a need to double check? > > Best regards, > Alfredo. > _______________________________________________ > 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 cecile.madjar at mcin.ca Tue Apr 9 10:08:34 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 9 Apr 2019 10:08:34 -0400 Subject: [Loris-dev] [IPMSA] Error: DBD::mysql::st execute failed: Incorrect date value: '' for column 'DateAcquired' In-Reply-To: References: Message-ID: Hi Alfredo, Could you take a look at the date field of your DICOMs? Is it possible that the date of acquisition was removed from the dataset? If so, this will be fixed with the release 20.3 of LORIS-MRI that should be released in April. In the meantime, you can take a look at the following PR that resolves all the issues in the insertion pipeline when no dates are available in a DICOM dataset: https://github.com/aces/Loris-MRI/pull/395 Hope this helps. Let me know how this goes or if you encounter additional issues! C?cile On Mon, Apr 8, 2019 at 6:37 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > I have 2 MRI sessions that could not be uploaded due to the following > error: > > -------------------------- > Use of uninitialized value $_ in pattern match (m//) at > /AAA/loris_data/IPMSA/bin/mri//batch_uploads_imageuploader line 92. > DBD::mysql::st execute failed: Incorrect date value: '' for column > 'DateAcquired' at row 1 at > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 238. > DBD::mysql::st execute failed: Cannot add or update a child row: a foreign > key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT > `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` > (`TarchiveID`) ON DELETE CASCADE) at > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. > DBD::mysql::st execute failed: Cannot add or update a child row: a foreign > key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT > `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` > (`TarchiveID`) ON DELETE CASCADE) at > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. > -------------------------- > > This is what I get in the log > file: /AAA/ANOM/CCC//log_batch_imageuploader_AAA10292_850501_w048.txt > -------------------------- > Running now the following command: > /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile > prod -upload_id 20872 /AAA/ANOM/CCC//AAA10292_850501_w048.tar.gz -verbose > > /AAA/loris_data/BBB/bin/mri/dicom-archive/dicomTar.pl > /tmp/ImagingUpload-12-4-kG9b0L /AAA/loris_data/BBB/data/tarchive -clobber > -database -profile prod -verbose > Source: /tmp/ImagingUpload-12-4-kG9b0L > Target: /AAA/loris_data/BBB/data/tarchive > > Testing for database connectivity. > Database is available. > > You will archive the dir : ImagingUpload-12-4-kG9b0L > > You are creating a tar with the following command: > tar -cf /AAA/loris_data/BBB/data/tarchive/ImagingUpload-12-4-kG9b0L.tar > ImagingUpload-12-4-kG9b0L > > > getting md5sums and gzipping!! > > * Taken from dir : /tmp/ImagingUpload-12-4-kG9b0L > * Archive target location : > /AAA/loris_data/BBB/tarchive/DCM__ImagingUpload-12-4-kG9b0L.tar > * Name of creating host : 132.216.133.49 > * Name of host OS : Linux > * Created by user : lorisadmin > * Archived on : 2019-04-07 12:05:46 > * dicomSummary version : 1 > * dicomTar version : 1 > * md5sum for DICOM tarball : 19fbaf1fcab253c3bdf741f4b7b5d4a2 > ImagingUpload-12-4-kG9b0L.tar > * md5sum for DICOM tarball gzipped : 3611bbab463663880c58fe32def90c8a > ImagingUpload-12-4-kG9b0L.tar.gz > * md5sum for complete archive : 2dc51a007126ad41e8e0195eda37a378 > DCM__ImagingUpload-12-4-kG9b0L.tar > > Adding archive info into database > Failed running query: INSERT INTO > tarchive SET DicomArchiveID = ?, PatientName = ?, > PatientID = ?, PatientDoB = ?, PatientGender = ?, > DateAcquired = ?, ScannerManufacturer = ?, ScannerModel = ?, > ScannerSerialNumber = ?, ScannerSoftwareVersion = ?, > CenterName = ?, AcquisitionCount = ?, NonDicomFileCount = > ?, DicomFileCount = ?, CreatingUser = ?, SourceLocation > = ?, sumTypeVersion = ?, AcquisitionMetadata = ?, > DateLastArchived = NOW() , tarTypeVersion = ?, md5sumArchive = > ?, md5sumDicomOnly = ?, ArchiveLocation = ?, CreateInfo = ? > , DateFirstArchived = NOW(), neurodbCenterName = > ? > > > > Removing temporary files from target location > > > The database command failed > > The dicomtar execution has failed > -------------------------- > > This cases were part of a list of 82 cases where 65 were correctly > uploaded (15 had another type of error that I just reported in a different > email). I can review the files with somebody from your team if required. > > Best regards, > Alfredo. > _______________________________________________ > 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 Fri Apr 12 11:48:04 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Fri, 12 Apr 2019 15:48:04 +0000 Subject: [Loris-dev] [IPMSA] Error: DBD::mysql::st execute failed: Incorrect date value: '' for column 'DateAcquired' In-Reply-To: References: , Message-ID: Dear C?cile, I checked the dicoms and we do have the Acquisition Date in every dicom file. Is there anything else I should check? Regards, Alfredo. ________________________________ From: Cecile Madjar Sent: Tuesday, April 9, 2019 10:08 AM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, Andrzej; Rozie Arnaoutelis, Ms.; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] Error: DBD::mysql::st execute failed: Incorrect date value: '' for column 'DateAcquired' External Email - Use Caution Hi Alfredo, Could you take a look at the date field of your DICOMs? Is it possible that the date of acquisition was removed from the dataset? If so, this will be fixed with the release 20.3 of LORIS-MRI that should be released in April. In the meantime, you can take a look at the following PR that resolves all the issues in the insertion pipeline when no dates are available in a DICOM dataset: https://github.com/aces/Loris-MRI/pull/395 Hope this helps. Let me know how this goes or if you encounter additional issues! C?cile On Mon, Apr 8, 2019 at 6:37 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, I have 2 MRI sessions that could not be uploaded due to the following error: -------------------------- Use of uninitialized value $_ in pattern match (m//) at /AAA/loris_data/IPMSA/bin/mri//batch_uploads_imageuploader line 92. DBD::mysql::st execute failed: Incorrect date value: '' for column 'DateAcquired' at row 1 at /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 238. DBD::mysql::st execute failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` (`TarchiveID`) ON DELETE CASCADE) at /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. DBD::mysql::st execute failed: Cannot add or update a child row: a foreign key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` (`TarchiveID`) ON DELETE CASCADE) at /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. -------------------------- This is what I get in the log file: /AAA/ANOM/CCC//log_batch_imageuploader_AAA10292_850501_w048.txt -------------------------- Running now the following command: /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 20872 /AAA/ANOM/CCC//AAA10292_850501_w048.tar.gz -verbose /AAA/loris_data/BBB/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-12-4-kG9b0L /AAA/loris_data/BBB/data/tarchive -clobber -database -profile prod -verbose Source: /tmp/ImagingUpload-12-4-kG9b0L Target: /AAA/loris_data/BBB/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-12-4-kG9b0L You are creating a tar with the following command: tar -cf /AAA/loris_data/BBB/data/tarchive/ImagingUpload-12-4-kG9b0L.tar ImagingUpload-12-4-kG9b0L getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-12-4-kG9b0L * Archive target location : /AAA/loris_data/BBB/tarchive/DCM__ImagingUpload-12-4-kG9b0L.tar * Name of creating host : 132.216.133.49 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-04-07 12:05:46 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 19fbaf1fcab253c3bdf741f4b7b5d4a2 ImagingUpload-12-4-kG9b0L.tar * md5sum for DICOM tarball gzipped : 3611bbab463663880c58fe32def90c8a ImagingUpload-12-4-kG9b0L.tar.gz * md5sum for complete archive : 2dc51a007126ad41e8e0195eda37a378 DCM__ImagingUpload-12-4-kG9b0L.tar Adding archive info into database Failed running query: INSERT INTO tarchive SET DicomArchiveID = ?, PatientName = ?, PatientID = ?, PatientDoB = ?, PatientGender = ?, DateAcquired = ?, ScannerManufacturer = ?, ScannerModel = ?, ScannerSerialNumber = ?, ScannerSoftwareVersion = ?, CenterName = ?, AcquisitionCount = ?, NonDicomFileCount = ?, DicomFileCount = ?, CreatingUser = ?, SourceLocation = ?, sumTypeVersion = ?, AcquisitionMetadata = ?, DateLastArchived = NOW() , tarTypeVersion = ?, md5sumArchive = ?, md5sumDicomOnly = ?, ArchiveLocation = ?, CreateInfo = ? , DateFirstArchived = NOW(), neurodbCenterName = ? Removing temporary files from target location The database command failed The dicomtar execution has failed -------------------------- This cases were part of a list of 82 cases where 65 were correctly uploaded (15 had another type of error that I just reported in a different email). I can review the files with somebody from your team if required. Best regards, Alfredo. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Fri Apr 12 11:55:38 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Fri, 12 Apr 2019 15:55:38 +0000 Subject: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. In-Reply-To: References: , Message-ID: Dear C?cile, I checked a couple of cases having this issue and they have the dicom field 0020,0032. Here is an example using dcmdump: (0020,0032) DS [-128.95269713082\-161.29539118652\87.7198252597444] # 50, 3 ImagePositionPatient Does this look good? Are there other field that I should check? Regards, Alfredo. ________________________________ From: Cecile Madjar Sent: Tuesday, April 9, 2019 10:05 AM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. External Email - Use Caution Hi Alfredo, I have a feeling you are encountering an issue that was fixed in release 20.2 of LORIS-MRI where DICOM files without the header (0020,0032) were automatically rejected by the script get_dicom_info.pl with the error message saying that the file is not a DICOM, while it is actually a DICOM... If you don't wish to upgrade your LORIS instance to 20.2 right away, you can take a look at the following PR that solved the issue: https://github.com/aces/Loris-MRI/pull/365 to implement the fix. Hope this helps! Let me know how it goes, C?cile On Mon, Apr 8, 2019 at 6:02 PM Morales Pinzon, Alfredo > wrote: Dear LoriDev team, Out of 82 MRI sessions that I was uploading into LORIS, 15 could not be uploaded due to the following error: --------------------------------------- Running now the following command: /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 20844 /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz -verbose /AAA/loris_data/IPMSA/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-9-29-1gMub2 /AAA/loris_data/BBB/data/tarchive -clobber -database -profile prod -verbose Source: /tmp/ImagingUpload-9-29-1gMub2 Target: /AAA/loris_data/BBB/data/tarchive Testing for database connectivity. Database is available. The target directory does not contain a single DICOM file. The dicomtar execution has failed --------------------------------------- I checked the file /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz and it has dicom files in it. Is there something a need to double check? Best regards, Alfredo. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Fri Apr 12 14:06:22 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Fri, 12 Apr 2019 14:06:22 -0400 Subject: [Loris-dev] [IPMSA] Error: DBD::mysql::st execute failed: Incorrect date value: '' for column 'DateAcquired' In-Reply-To: References: Message-ID: Hi Alfredo, That is strange. Maybe the date in the DICOM files is weird. Are you planning on coming to the LORIS meeting on Tuesday? If so, maybe we could meet before the meeting and try to see what is going on? Let me know. Thanks! On Fri, Apr 12, 2019 at 11:48 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear C?cile, > > I checked the dicoms and we do have the Acquisition Date in every dicom > file. Is there anything else I should check? > > Regards, > Alfredo. > ------------------------------ > *From:* Cecile Madjar > *Sent:* Tuesday, April 9, 2019 10:08 AM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, > Andrzej; Rozie Arnaoutelis, Ms.; Zografos Caramanos; Douglas Arnold, Dr.; > Guttmann, Charles,M.D. > *Subject:* Re: [Loris-dev] [IPMSA] Error: DBD::mysql::st execute failed: > Incorrect date value: '' for column 'DateAcquired' > > > External Email - Use Caution > > Hi Alfredo, > > Could you take a look at the date field of your DICOMs? Is it possible > that the date of acquisition was removed from the dataset? > > If so, this will be fixed with the release 20.3 of LORIS-MRI that should > be released in April. In the meantime, you can take a look at the following > PR that resolves all the issues in the insertion pipeline when no dates are > available in a DICOM dataset: https://github.com/aces/Loris-MRI/pull/395 > > Hope this helps. > Let me know how this goes or if you encounter additional issues! > > C?cile > > On Mon, Apr 8, 2019 at 6:37 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear LorisDev team, > > I have 2 MRI sessions that could not be uploaded due to the following > error: > > -------------------------- > Use of uninitialized value $_ in pattern match (m//) at > /AAA/loris_data/IPMSA/bin/mri//batch_uploads_imageuploader line 92. > DBD::mysql::st execute failed: Incorrect date value: '' for column > 'DateAcquired' at row 1 at > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 238. > DBD::mysql::st execute failed: Cannot add or update a child row: a foreign > key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT > `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` > (`TarchiveID`) ON DELETE CASCADE) at > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. > DBD::mysql::st execute failed: Cannot add or update a child row: a foreign > key constraint fails (`IPMSA_LORIS`.`tarchive_series`, CONSTRAINT > `tarchive_series_ibfk_1` FOREIGN KEY (`TarchiveID`) REFERENCES `tarchive` > (`TarchiveID`) ON DELETE CASCADE) at > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 324. > -------------------------- > > This is what I get in the log > file: /AAA/ANOM/CCC//log_batch_imageuploader_AAA10292_850501_w048.txt > -------------------------- > Running now the following command: > /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile > prod -upload_id 20872 /AAA/ANOM/CCC//AAA10292_850501_w048.tar.gz -verbose > > /AAA/loris_data/BBB/bin/mri/dicom-archive/dicomTar.pl > /tmp/ImagingUpload-12-4-kG9b0L /AAA/loris_data/BBB/data/tarchive -clobber > -database -profile prod -verbose > Source: /tmp/ImagingUpload-12-4-kG9b0L > Target: /AAA/loris_data/BBB/data/tarchive > > Testing for database connectivity. > Database is available. > > You will archive the dir : ImagingUpload-12-4-kG9b0L > > You are creating a tar with the following command: > tar -cf /AAA/loris_data/BBB/data/tarchive/ImagingUpload-12-4-kG9b0L.tar > ImagingUpload-12-4-kG9b0L > > > getting md5sums and gzipping!! > > * Taken from dir : /tmp/ImagingUpload-12-4-kG9b0L > * Archive target location : > /AAA/loris_data/BBB/tarchive/DCM__ImagingUpload-12-4-kG9b0L.tar > * Name of creating host : 132.216.133.49 > * Name of host OS : Linux > * Created by user : lorisadmin > * Archived on : 2019-04-07 12:05:46 > * dicomSummary version : 1 > * dicomTar version : 1 > * md5sum for DICOM tarball : 19fbaf1fcab253c3bdf741f4b7b5d4a2 > ImagingUpload-12-4-kG9b0L.tar > * md5sum for DICOM tarball gzipped : 3611bbab463663880c58fe32def90c8a > ImagingUpload-12-4-kG9b0L.tar.gz > * md5sum for complete archive : 2dc51a007126ad41e8e0195eda37a378 > DCM__ImagingUpload-12-4-kG9b0L.tar > > Adding archive info into database > Failed running query: INSERT INTO > tarchive SET DicomArchiveID = ?, PatientName = ?, > PatientID = ?, PatientDoB = ?, PatientGender = ?, > DateAcquired = ?, ScannerManufacturer = ?, ScannerModel = ?, > ScannerSerialNumber = ?, ScannerSoftwareVersion = ?, > CenterName = ?, AcquisitionCount = ?, NonDicomFileCount = > ?, DicomFileCount = ?, CreatingUser = ?, SourceLocation > = ?, sumTypeVersion = ?, AcquisitionMetadata = ?, > DateLastArchived = NOW() , tarTypeVersion = ?, md5sumArchive = > ?, md5sumDicomOnly = ?, ArchiveLocation = ?, CreateInfo = ? > , DateFirstArchived = NOW(), neurodbCenterName = > ? > > > > Removing temporary files from target location > > > The database command failed > > The dicomtar execution has failed > -------------------------- > > This cases were part of a list of 82 cases where 65 were correctly > uploaded (15 had another type of error that I just reported in a different > email). I can review the files with somebody from your team if required. > > Best regards, > Alfredo. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > 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. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Fri Apr 12 14:19:57 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Fri, 12 Apr 2019 14:19:57 -0400 Subject: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. In-Reply-To: References: Message-ID: Hi again, Could we look into this issue together on Tuesday too? Not entirely sure why you get this error but we'll find out!! Thanks! C?cile On Fri, Apr 12, 2019 at 11:55 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear C?cile, > > I checked a couple of cases having this issue and they have the dicom > field 0020,0032. Here is an example using dcmdump: > > (0020,0032) DS [-128.95269713082\-161.29539118652\87.7198252597444] # 50, > 3 ImagePositionPatient > > Does this look good? Are there other field that I should check? > > Regards, > Alfredo. > > ------------------------------ > *From:* Cecile Madjar > *Sent:* Tuesday, April 9, 2019 10:05 AM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie > Arnaoutelis; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, > Charles,M.D. > *Subject:* Re: [Loris-dev] [IPMSA] Error: The target directory does not > contain a single DICOM file. > > > External Email - Use Caution > > Hi Alfredo, > > I have a feeling you are encountering an issue that was fixed in release > 20.2 of LORIS-MRI where DICOM files without the header (0020,0032) were > automatically rejected by the script get_dicom_info.pl with the error > message saying that the file is not a DICOM, while it is actually a DICOM... > > If you don't wish to upgrade your LORIS instance to 20.2 right away, you > can take a look at the following PR that solved the issue: > https://github.com/aces/Loris-MRI/pull/365 to implement the fix. > > Hope this helps! Let me know how it goes, > > C?cile > > > > On Mon, Apr 8, 2019 at 6:02 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear LoriDev team, > > Out of 82 MRI sessions that I was uploading into LORIS, 15 could not be > uploaded due to the following error: > > --------------------------------------- > Running now the following command: > /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile > prod -upload_id 20844 /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz > -verbose > > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/dicomTar.pl > /tmp/ImagingUpload-9-29-1gMub2 /AAA/loris_data/BBB/data/tarchive -clobber > -database -profile prod -verbose > Source: /tmp/ImagingUpload-9-29-1gMub2 > Target: /AAA/loris_data/BBB/data/tarchive > > Testing for database connectivity. > Database is available. > > The target directory does not contain a single DICOM file. > > The dicomtar execution has failed > --------------------------------------- > > I checked the file /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz and > it has dicom files in it. Is there something a need to double check? > > Best regards, > Alfredo. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > 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. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Fri Apr 12 15:29:54 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Fri, 12 Apr 2019 19:29:54 +0000 Subject: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. In-Reply-To: References: , Message-ID: Hi C?cile, It's great we can look into this together but, as I am based in Boston, we would need to do it by video call. I don't remember exactly the time for LORIS meeting, but I can make myself available anytime. Just let me know what works the best for you. Thank you for quick reply and help. Regards, Alfredo. ________________________________ From: Cecile Madjar Sent: Friday, April 12, 2019 2:19 PM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. External Email - Use Caution Hi again, Could we look into this issue together on Tuesday too? Not entirely sure why you get this error but we'll find out!! Thanks! C?cile On Fri, Apr 12, 2019 at 11:55 AM Morales Pinzon, Alfredo > wrote: Dear C?cile, I checked a couple of cases having this issue and they have the dicom field 0020,0032. Here is an example using dcmdump: (0020,0032) DS [-128.95269713082\-161.29539118652\87.7198252597444] # 50, 3 ImagePositionPatient Does this look good? Are there other field that I should check? Regards, Alfredo. ________________________________ From: Cecile Madjar > Sent: Tuesday, April 9, 2019 10:05 AM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie Arnaoutelis; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. External Email - Use Caution Hi Alfredo, I have a feeling you are encountering an issue that was fixed in release 20.2 of LORIS-MRI where DICOM files without the header (0020,0032) were automatically rejected by the script get_dicom_info.pl with the error message saying that the file is not a DICOM, while it is actually a DICOM... If you don't wish to upgrade your LORIS instance to 20.2 right away, you can take a look at the following PR that solved the issue: https://github.com/aces/Loris-MRI/pull/365 to implement the fix. Hope this helps! Let me know how it goes, C?cile On Mon, Apr 8, 2019 at 6:02 PM Morales Pinzon, Alfredo > wrote: Dear LoriDev team, Out of 82 MRI sessions that I was uploading into LORIS, 15 could not be uploaded due to the following error: --------------------------------------- Running now the following command: /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 20844 /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz -verbose /AAA/loris_data/IPMSA/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-9-29-1gMub2 /AAA/loris_data/BBB/data/tarchive -clobber -database -profile prod -verbose Source: /tmp/ImagingUpload-9-29-1gMub2 Target: /AAA/loris_data/BBB/data/tarchive Testing for database connectivity. Database is available. The target directory does not contain a single DICOM file. The dicomtar execution has failed --------------------------------------- I checked the file /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz and it has dicom files in it. Is there something a need to double check? Best regards, Alfredo. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Fri Apr 12 15:35:52 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Fri, 12 Apr 2019 15:35:52 -0400 Subject: [Loris-dev] [IPMSA] Error: The target directory does not contain a single DICOM file. In-Reply-To: References: Message-ID: Oups, sorry, I did not realize. How about a call with Zoom on Monday then? This way we'll be able to share screens. Let me know what time works for you. On Fri, Apr 12, 2019 at 3:30 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi C?cile, > > It's great we can look into this together but, as I am based in Boston, we > would need to do it by video call. I don't remember exactly the time for > LORIS meeting, but I can make myself available anytime. Just let me know > what works the best for you. > > Thank you for quick reply and help. > > Regards, > Alfredo. > ------------------------------ > *From:* Cecile Madjar > *Sent:* Friday, April 12, 2019 2:19 PM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie > Arnaoutelis; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, > Charles,M.D. > *Subject:* Re: [Loris-dev] [IPMSA] Error: The target directory does not > contain a single DICOM file. > > > External Email - Use Caution > > Hi again, > > Could we look into this issue together on Tuesday too? Not entirely sure > why you get this error but we'll find out!! > > Thanks! > > C?cile > > On Fri, Apr 12, 2019 at 11:55 AM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear C?cile, > > I checked a couple of cases having this issue and they have the dicom > field 0020,0032. Here is an example using dcmdump: > > (0020,0032) DS [-128.95269713082\-161.29539118652\87.7198252597444] # 50, > 3 ImagePositionPatient > > Does this look good? Are there other field that I should check? > > Regards, > Alfredo. > > ------------------------------ > *From:* Cecile Madjar > *Sent:* Tuesday, April 9, 2019 10:05 AM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Rozie > Arnaoutelis; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, > Charles,M.D. > *Subject:* Re: [Loris-dev] [IPMSA] Error: The target directory does not > contain a single DICOM file. > > > External Email - Use Caution > > Hi Alfredo, > > I have a feeling you are encountering an issue that was fixed in release > 20.2 of LORIS-MRI where DICOM files without the header (0020,0032) were > automatically rejected by the script get_dicom_info.pl with the error > message saying that the file is not a DICOM, while it is actually a DICOM... > > If you don't wish to upgrade your LORIS instance to 20.2 right away, you > can take a look at the following PR that solved the issue: > https://github.com/aces/Loris-MRI/pull/365 to implement the fix. > > Hope this helps! Let me know how it goes, > > C?cile > > > > On Mon, Apr 8, 2019 at 6:02 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear LoriDev team, > > Out of 82 MRI sessions that I was uploading into LORIS, 15 could not be > uploaded due to the following error: > > --------------------------------------- > Running now the following command: > /AAA/loris_data/BBB/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile > prod -upload_id 20844 /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz > -verbose > > /AAA/loris_data/IPMSA/bin/mri/dicom-archive/dicomTar.pl > /tmp/ImagingUpload-9-29-1gMub2 /AAA/loris_data/BBB/data/tarchive -clobber > -database -profile prod -verbose > Source: /tmp/ImagingUpload-9-29-1gMub2 > Target: /AAA/loris_data/BBB/data/tarchive > > Testing for database connectivity. > Database is available. > > The target directory does not contain a single DICOM file. > > The dicomtar execution has failed > --------------------------------------- > > I checked the file /AAA/ANOM/STUDYNAME//AAA10026_343633_w024.tar.gz and > it has dicom files in it. Is there something a need to double check? > > Best regards, > Alfredo. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > 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. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Apr 15 18:17:10 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 15 Apr 2019 22:17:10 +0000 Subject: [Loris-dev] [IPMSA] MINC extent Message-ID: Dear LORIS-dev team, We have found an issue with some images where the created MINC file in LORIS only contains 1 slice. We have identified the potential error, which comes from the DICOM files, but we would like to track the images imported into LORIS having this problem. Is the information about the extend of the images saved in the database? What would be the best strategy to find these images. 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 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Apr 16 10:08:30 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 16 Apr 2019 10:08:30 -0400 Subject: [Loris-dev] [IPMSA] MINC extent In-Reply-To: References: Message-ID: Dear Alfredo, This can easily be done using an SQL query since every header present in the MINC files are inserted into the parameter_file table. Quick review of the MRI tables' structure (tables that you will need to query): - files => stores the path to the file and some basic information. Primary key = FileID - parameter_type => stores the data dictionary of LORIS. Primary key = ParameterTypeID (all MINC header names can be found in this table when you add (WHERE SourceFrom="parameter_file") - parameter_file => stores all files MINC header values. Foreign keys to the files and parameter_type tables being the FileID and ParameterTypeID columns of parameter_file. The Value column would store the MINC header value So basically, to query the files matching a specific value for a MINC header, you would use a query like this one: SELECT File, Value FROM files f JOIN parameter_file pf USING (FileID) JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="YOUR MINC HEADER NAME HERE" AND pf.Value="THE VALUE YOU WANT TO RESTRICT THE QUERY ON" In blue are the part that you will need to populate based on what you are looking for. For example, if you want to select all files with a repetition time of 2000ms, you would use the following values: - pt.Name="acquisition:repetition_time" - pf.Value="2000" Hope this helps. Let me know if something is not clear or if you have additional questions. Best, C?cile On Mon, Apr 15, 2019 at 6:17 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LORIS-dev team, > > We have found an issue with some images where the created MINC file in > LORIS only contains 1 slice. We have identified the potential error, which > comes from the DICOM files, but we would like to track the images imported > into LORIS having this problem. Is the information about the extend of the > images saved in the database? What would be the best strategy to find these > images. > > 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 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: From AMORALESPINZON at bwh.harvard.edu Wed Apr 17 14:22:16 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 17 Apr 2019 18:22:16 +0000 Subject: [Loris-dev] [IPMSA] MINC extent In-Reply-To: References: , Message-ID: Dear C?cile, Thank you for explanation! Very helpful. I was able to put the right values and get the query that we needed. Regards, Alfredo. ________________________________ From: Cecile Madjar Sent: Tuesday, April 16, 2019 10:08 AM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, Andrzej; Rozie Arnaoutelis; Zografos Caramanos; Douglas Arnold, Dr.; Guttmann, Charles,M.D.; Samson Antel Subject: Re: [Loris-dev] [IPMSA] MINC extent External Email - Use Caution Dear Alfredo, This can easily be done using an SQL query since every header present in the MINC files are inserted into the parameter_file table. Quick review of the MRI tables' structure (tables that you will need to query): * files => stores the path to the file and some basic information. Primary key = FileID * parameter_type => stores the data dictionary of LORIS. Primary key = ParameterTypeID (all MINC header names can be found in this table when you add (WHERE SourceFrom="parameter_file") * parameter_file => stores all files MINC header values. Foreign keys to the files and parameter_type tables being the FileID and ParameterTypeID columns of parameter_file. The Value column would store the MINC header value So basically, to query the files matching a specific value for a MINC header, you would use a query like this one: SELECT File, Value FROM files f JOIN parameter_file pf USING (FileID) JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name="YOUR MINC HEADER NAME HERE" AND pf.Value="THE VALUE YOU WANT TO RESTRICT THE QUERY ON" In blue are the part that you will need to populate based on what you are looking for. For example, if you want to select all files with a repetition time of 2000ms, you would use the following values: * pt.Name="acquisition:repetition_time" * pf.Value="2000" Hope this helps. Let me know if something is not clear or if you have additional questions. Best, C?cile On Mon, Apr 15, 2019 at 6:17 PM Morales Pinzon, Alfredo > wrote: Dear LORIS-dev team, We have found an issue with some images where the created MINC file in LORIS only contains 1 slice. We have identified the potential error, which comes from the DICOM files, but we would like to track the images imported into LORIS having this problem. Is the information about the extend of the images saved in the database? What would be the best strategy to find these images. 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 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: From AMORALESPINZON at bwh.harvard.edu Fri Apr 19 08:41:24 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Fri, 19 Apr 2019 12:41:24 +0000 Subject: [Loris-dev] [IPMSA] Import from BIDS Message-ID: Dear LORIS-Dev team, We would like to know if LORIS is able to import images from a trial/study in BIDS format. So far we have used DICOM to import images from different trial/studies but we might have a couple of studies where BIDS is the only available source of images. I would like to clarify that we are talking about source images, not processed data. 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 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Fri Apr 19 18:38:17 2019 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Fri, 19 Apr 2019 18:38:17 -0400 Subject: [Loris-dev] [IPMSA] Import from BIDS In-Reply-To: References: Message-ID: Hi Alfredo - Just a quick response as most of us are out of the office until Tuesday. LORIS has tools for importing BIDS EEG data (e.g. see Loris-MRI 20.2 ), and later this year we plan to add BIDS support for MRI. If you'd like guidance on adapting the current BIDS-EEG scripts for other modalities sooner, let us know. Best, Christine On Fri, Apr 19, 2019 at 8:41 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LORIS-Dev team, > > We would like to know if LORIS is able to import images from a trial/study > in BIDS format. So far we have used DICOM to import images from different > trial/studies but we might have a couple of studies where BIDS is the only > available source of images. I would like to clarify that we are talking > about source images, not processed data. > > 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 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 > -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Tue Apr 23 09:19:50 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 23 Apr 2019 13:19:50 +0000 Subject: [Loris-dev] [IPMSA] Import from BIDS In-Reply-To: References: , Message-ID: Hi Christine, Thank you for you quick answer. We will get back to you in case we need your assistance with BIDS support for MRI. Best regards, Alfredo. ________________________________ From: Christine Rogers Sent: Friday, April 19, 2019 6:38 PM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; Rozie Arnaoutelis; Sridar Narayanan, Dr.; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [IPMSA] Import from BIDS External Email - Use Caution Hi Alfredo - Just a quick response as most of us are out of the office until Tuesday. LORIS has tools for importing BIDS EEG data (e.g. see Loris-MRI 20.2), and later this year we plan to add BIDS support for MRI. If you'd like guidance on adapting the current BIDS-EEG scripts for other modalities sooner, let us know. Best, Christine On Fri, Apr 19, 2019 at 8:41 AM Morales Pinzon, Alfredo > wrote: Dear LORIS-Dev team, We would like to know if LORIS is able to import images from a trial/study in BIDS format. So far we have used DICOM to import images from different trial/studies but we might have a couple of studies where BIDS is the only available source of images. I would like to clarify that we are talking about source images, not processed data. 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 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 -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: