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| − | Contact: Mark Anderson | + | '''Contact:''' Mark Anderson (mark at bwh.harvard.edu) |
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| − | <center>
| + | ==Sending images from BWH scanners to SPL (DICOM)== |
| − | '''Pushing images from scanners to SPL (DICOM)'''
| + | This is the method for researchers and clinicians to get their data to the SPL after a scan has been done. Most of the scanners have been configured to allow images to be sent to the SPL. The user name of the sender of the images is recorded to maintain HIPAA compliance. At the scanner, select either LISA or SPL as the DICOM destination and transfer the images. Data will be sent to the directory /spl/tmp/incoming/processed. If non-clinical scans are not transferred to the SPL or stored on MOD, there is a good chance the data will be deleted unless a prominent note is left for the technicians and they are reminded not to delete the data. Clinical cases are archived and can be restored via the following method. |
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| − | </center>
| + | ==Restoring images from PACS from 2002 -present (DICOM)== |
| − | This is a good way for researchers to get their data to the SPL after a scan has been done. Most of the scanners have been configured to allow images to be sent to the SPL. The user name of the sender of the images is recorded to maintain HIPAA compliance. At the scanner select either LISA or SPL as the DICOM destination and transfer the images. Data will be sent to the directory /spl/tmp/incoming. If there is a lot of data in /spl/tmp/incoming it may take a while to locate your particular case. One method is to find timestamps on files in /spl/tmp/incoming that match the time that the images were transferred from the scanners or see the section below "Finding DICOM data in /spl/tmp/incoming after it has been transferred". If non-clinical scans are not transferred to the SPL or stored on MOD, there is a good chance the data will be deleted unless a prominent note is left for the techs and they are reminded not to delete the data. Clinical cases are archived and can be restored via the following method. | + | This is the best way to get all CT, MR, and PET or PET/CT images from approximately the beginning of 2002 to present that are not on the scanners. |
| | + | Data will be sent to the SPL directory /spl/tmp/incoming/processed via a web-based IMPAX service tool. |
| | + | Send email to Mark Anderson (mark at bwh.harvard.edu)to get cases transferred via this method. The information to send is the Accession number of |
| | + | the scan, or if the Accession number is not known, use the MRN and date of the scan. |
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| − | <center>
| + | ==Finding DICOM data in /spl/tmp/incoming/processed after it has been transferred== |
| − | '''Restoring images from PACS from 09/1998-present (DICOM)'''
| + | A file called |
| − | </center>
| + | /spl/tmp/incoming/processed/studylist |
| − | This is the best way to get all CT and MR images from September 1998 to present that are not on the scanners. Data can be sent to SPL directly to /spl/tmp/incoming from any of the IMPAX systems in the reading rooms or from a web-based IMPAX service tool. Send email to [mailto:mark@bwh.harvard.edu mark@bwh.harvard.edu]
| + | is updated every 10 minutes describing all data currently completely transferred to SPL and processed into |
| − | or [mailto:marianna@bwh.harvard.edu marianna@bwh.harvard.edu]
| + | a hierarchy of /study/series/images for research data or /accession_number/series/image for clinical data. Below is an example of one entry |
| − | to get cases transferred via this method. If you plan to use this method frequently, you may want to get your own BICS account with transfer privileges by calling the help desk at x2-5927 | + | in the file /spl/tmp/incoming/processed/studylist for a research study of a phantom scan with a study number of 1234: |
| − | <center>
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| − | '''Finding DICOM data in /spl/tmp/incoming after it has been transferred'''
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| − | </center>
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| − | The easiest way to find your DICOM data is to point your browser to /spl/tmp/incoming/ and look for a file with a name beginning with
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| − | DICOM_files_as_of
| + | data for subject PHANTOM with patient id PHANTOM is in directory /spl/tmp/incoming/processed/1234 |
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| − | The file name will contain a time stamp and look similar to the filename below. | + | The file system /spl/tmp/incoming/processed contains fifty gigabytes of space. The data persists in /spl/tmp/incoming/processed for one week from the time it is acquired and is automatically deleted after one week. |
| − | <center>
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| − | DICOM_files_as_of:12_30_04_at_14:10:28.html
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| − | </center>
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| − | This file is updated every hour on the hour with a list of the current contents of /spl/tmp/incoming/ and the time that the file was updated is part of the file name. The above file shows the contents of /spl/tmp/incoming as of Dec 30 2004 at 2:10 in the afteroon. After clicking on the DICOM html you will see information similar to the following which should help you to locate your data. One way to use the page similar to the one below is to do the following:
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| − | * open a command window and change to the Root Directory in the window (e.g cd /spl/tmp/incoming)
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| − | * load the DICOM_files_as_of:**********.html page into your browser
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| − | * use the edit->Find in This Page tab of the browser and type in the Patient ID or Patient Name. If you get the Alert message "The text you entered was not found." Then either you have entered the incorrect information or you will need to wait until the page is updated on the next hour.
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| − | * If your Patient Name or Patient ID is found in DICOM html then cut and paste from the DICOM html page the path above the Patient Name or Patient ID pointing to where your data is located and change to that directory(e.g. cd MR0000.MOD/LMRC3T.STA/20050623.DAY/1.2.840.113619.2.136.1762888421.2231.1119526620.0.UID/)
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| − | * from this directory, copy your data to a safe place as it will be deleted 1 week after it is last accessed
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| − | <center>
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| − | [[Image:image_info.jpg]]
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| − | </center>
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| − | Below is an example of how the directories might be organized in /spl/tmp/incoming:
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| − | ./MR0000.MOD/BWOW1.STA
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| − | ./MR0000.MOD/BWOW1.STA/20040609.DAY
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| − | ./MR0000.MOD/BWOW1.STA/20040609.DAY/1.2.840.113619.2.5.1762874864.1706.1086778760.584.UID
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| − | ./MR0000.MOD/BWOW1.STA/20040609.DAY/1.2.840.113619.2.5.1762874864.1706.1086778760.584.UID/000001.SER
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| − | ./MR0000.MOD/BWOW1.STA/20040609.DAY/1.2.840.113619.2.5.1762874864.1706.1086778760.584.UID/000002.SER
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| − | ./MR0000.MOD/BWOW1.STA/20040609.DAY/1.2.840.113619.2.5.1762874864.1706.1086778760.584.UID/000003.SER
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| − | ./MR0000.MOD/BWOW1.STA/20040609.DAY/1.2.840.113619.2.5.1762874864.1706.1086778760.584.UID/000005.SER
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| − | ./MR0000.MOD/BWOW1.STA/20040609.DAY/1.2.840.113619.2.5.1762874864.1706.1086778760.584.UID/000006.SER
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| − | ./CT0000.MOD
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| − | ./CT0000.MOD/BWCTPIKE.STA
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| − | ./CT0000.MOD/BWCTPIKE.STA/20040610.DAY
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| − | ./CT0000.MOD/BWCTPIKE.STA/20040610.DAY/1.3.12.2.1107.5.1.4.28154.4.0.4973204933331248.UID
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| − | ./CT0000.MOD/BWCTPIKE.STA/20040610.DAY/1.3.12.2.1107.5.1.4.28154.4.0.4973204933331248.UID/000002.SER
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| − | The following describes the hierarchy of the directories (we will use the CT0000.MOD directory above as an example)
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| − | * CT0000.MOD this is the modality usually either CT or MR for most SPL data
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| − | * BWCTPIKE.STA this is the StationName where the image was transferred from.
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| − | * 20040610.DAY The date of the scan. This scan was done on June 10, 2004.
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| − | * 1.3.12.2.1107.5.1.4.28154.4.0.4973204933331248.UID This annoyingly long string is called the StudyInstanceUID and it uniquely identifies this study. This string does not provide much useful information to most users. The beginning part of the string (1.3.12.2.1107.5.1.4) is the Implementation Class UID and identifies the images in this directory as coming from a Siemens scanner.
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| − | Software Available for Sharing
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| − | The software used here is comprised of three main parts:
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| − | 1) A proprietary DICOM listener that recieves the data. We have a licence for this from the Dejarnette Corporation, this is not sharable.
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| − | 2) print_header program that gleans information from DICOM image headers. This is our software and is available for sharing and runs on Solaris and Linux.
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| − | 3) A series of shell and python scripts that collect the image information and generate a web page describing the data. This software is very specific to our site and likely not useful elsewhere.
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Contact: Mark Anderson (mark at bwh.harvard.edu)
Sending images from BWH scanners to SPL (DICOM)
This is the method for researchers and clinicians to get their data to the SPL after a scan has been done. Most of the scanners have been configured to allow images to be sent to the SPL. The user name of the sender of the images is recorded to maintain HIPAA compliance. At the scanner, select either LISA or SPL as the DICOM destination and transfer the images. Data will be sent to the directory /spl/tmp/incoming/processed. If non-clinical scans are not transferred to the SPL or stored on MOD, there is a good chance the data will be deleted unless a prominent note is left for the technicians and they are reminded not to delete the data. Clinical cases are archived and can be restored via the following method.
Restoring images from PACS from 2002 -present (DICOM)
This is the best way to get all CT, MR, and PET or PET/CT images from approximately the beginning of 2002 to present that are not on the scanners.
Data will be sent to the SPL directory /spl/tmp/incoming/processed via a web-based IMPAX service tool.
Send email to Mark Anderson (mark at bwh.harvard.edu)to get cases transferred via this method. The information to send is the Accession number of
the scan, or if the Accession number is not known, use the MRN and date of the scan.
Finding DICOM data in /spl/tmp/incoming/processed after it has been transferred
A file called
/spl/tmp/incoming/processed/studylist
is updated every 10 minutes describing all data currently completely transferred to SPL and processed into
a hierarchy of /study/series/images for research data or /accession_number/series/image for clinical data. Below is an example of one entry
in the file /spl/tmp/incoming/processed/studylist for a research study of a phantom scan with a study number of 1234:
data for subject PHANTOM with patient id PHANTOM is in directory /spl/tmp/incoming/processed/1234
The file system /spl/tmp/incoming/processed contains fifty gigabytes of space. The data persists in /spl/tmp/incoming/processed for one week from the time it is acquired and is automatically deleted after one week.
