Uploading Instructions

Content
Overview
Registration
Data Formating
Uploading

Overview

We accept submissions of deidentified BOLD, DTI and T1 data from registered users. Although ftp downloading is available for all site visitors at ftp://www.openpain.org without registration, additional data can only be uploaded following a registration procedure on the site homepage. Registration will send your contact information to the Open Pain Project curator who will provide a temporary password protected account for your personal use.

You may then upload and download private data using this account, without immediately releasing your data directly to the public ftp. It is the data contributor's responsibility to deidentify and format data appropriately before uploading, but our site curator will also inspect recently uploaded data to ensure compliance with the Open Pain Project's standards. Once the curator and contributor are both satisfied with the state of the data uploaded, the curator will move it to the public ftp for distribution.

The only requirements the Open Pain Project places on the content of uploaded BOLD, DTI or T1 data are that it be properly deidentified and that it be associated with a published paper detailing scanning and experimental procedures. However, to ensure greatest visibility, accessibility, and expedite turnaround times from initial upload to publication, we additionally ask data contributors to follow certain formating guidelines. The instructions contained here are meant to guide the uploader through registration for an ftp account, the process of deidentifying, formating and structuring their data before an upload, and the actual upload process itself.

Registration

Registration can be accomplished by submitting the following information through the form available on the Open Pain Project's home page.

  • name
  • institutional affiliation
  • email address
Once registered the database curator will contact you with further instructions.

Data Formating

All imaging data on the Open Pain Project is stored in nifti format (extension: *.nii or *.nii.gz). Conversion from DICOM to NIFTI is possible using the dcm2nii converter.

This software can also be used to remove basic identifying information stored in the DICOM format used by most MR scanners such as names, date of birth and gender, however this does not necessarily cover all potentially identifying information which might be embedded in your DICOM data.

In addition to raw imaging data DICOM data also contains a set of tags with established structure that contain elements pertaining to the image collection and subject, including potentially subject identifying information. The United States Health Insurance Portability and Accountability Act (HIPAA) specifies 18 types of potentially identifying information which should be removed. The tag elements of DICOM files which contain HIPAA prohibited content are sufficiently well defined that simple automated software processes like those implemented by dcm2nii can remove this information, however there are also 'private tags' in which manufacturers can insert data of their own. These private tags are susceptible to misuse and no agreed upon generalizable method exists to remove the information. The conversion to nifti using dcm2nii should not include such private field data in the nifti file, but it is the contributor's responsibility to be aware of this risk and take appropriate precautions to prevent the release of identifying information.

In addition, there is a possibility of identifying an individual based on facial characteristics rendered from high resolution MRI images. Consequently, facial features should to be removed before publication of a dataset. Our standard method for defacing involves applying spatial filters to "blur" faces in T1 data using tools developed by the Neuroinformatics Research Group (NRG) at Washington University in St Louis, and we will implement this for you prior to data publication if you provide us with non-defaced data. If you wish to implement this procedure yourself, the appropriate matlab scripts can be obtained from the NRG website. Although alternative defacing methods such as skull stripping are possible, facial masking using the NRG algorithm is the preferred method for facial deidentification for the Open Pain Project.

Metadata related to imaging data should accompany all datasets. Metadata is supplementary information such as behavioral parameters or demographic data, and is stored in a series of plain text or in comma separated variable (CSV) files. Critical metadata which should be collected before assembling a dataset for upload includes at least the following

  • age and gender of all subjects
  • a task file describing whatever task is performed by subjects and designating the task identifier label used in the dataset
  • relevant scanning parameters such as repetition time (TR)
  • a citation of a published paper in which the dataset is described and/or analyzed
  • a usage license. An example can be found in ftp://openpain.org/thermal/

Data should be organized in a hierarchical folder structure according to OpenfMRI project's organizational scheme outlined in their methods paper (see figure 1 therein). An example of our own is available at ftp://openpain.org/thermal/.

Uploading

Following registration the Open Pain Project curator will receive your information and create an ftp account for you. You will then be contacted by email regarding your authentication information and permission to begin uploading data. Once finished you should notify the site curator by responding to this email so that your data may be inspected and uploaded.

The method through which you upload the data itself will vary by operating system. The most secure method is to use sftp, which is ftp wrapped in a cryptographically secure tunnel, but requires specialized software under Windows and OS X. Standard FTP uploading is also possible for those who are so inclined, but because it is an insecure upload method instructions will not be provided for its use.

MS Windows:

Many free SFTP clients are available for download. We recommend WinSCP.

Upon running the program you'll be prompted for a host name, username and password. The hostname is openpain.org. The username and password are those which were provided for you by the site curator. All settings can be left in their default state. During your first connection you will be prompted with a security verification dialog. Accept it to access your directory on the Open Pain Project's FTP server.

Once the connection is established you will see your remote directory in the right pane juxtaposed against your local files in the left pane. To copy files to the server simply drag and drop from the left to the right pane. Your initial login directory is /home/<username>. You should upload your files here or into a subdirectory of this folder you create. You will not have write access outside of /home/<username>. Please upload your files as a complete directory structure not in an archived dataformat like a zip file.

OS X

OS X does not have native sftp support. Download cyberduck instead. Either download the installer and install the program, or download and run the standalone *zip file.

Once running cyberduck click "open connection" in the top left corner of your cyberduck instance. You will be prompted with a window containing login windows. From the drop down menu at the top of this window select "SFTP (SSH File Transfer Protocol)". In the remaining fields specify openpain.org for the server, and enter the username and password provided by the curator. Hit "connect" and accept the security prompt.

Your default directory upon connecting will be /home/<username>. You should drag and drop your dataset here or into a subfolder. Subfolders can be created with SHIFT+command+N. You will not have write access outside of /home/<username>. Please upload your files as a complete directory structure not in an archived dataformat like a zip file.

Unix or Linux:

sftp is natively supported under most *nix operating systems. Please speak with your system administrator regarding the specific procedure you should follow.

Helpful Reference

Poldrack R a, Barch DM, Mitchell JP, et al. Toward open sharing of task-based fMRI data: the OpenfMRI project. Front. Neuroinform. 2013;7(July):12. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3703526&tool=pmcentrez&rendertype=abstract. Accessed November 6, 2013.

HIPAA Identifiers

  • Names
  • All geographical subdivisions smaller than a State, including street address, city, county, precinct, zip code, and their equivalent geocodes, except for the initial three digits of a zip code, if according to the current publicly available data from the Bureau of the Census: (1) The geographic unit formed by combining all zip codes with the same three initial digits contains more than 20,000 people; and (2) The initial three digits of a zip code for all such geographic units containing 20,000 or fewer people is changed to 000.
  • All elements of dates (except year) for dates directly related to an individual, including birth date, admission date, discharge date, date of death; and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older
  • Phone numbers
  • Fax numbers
  • Electronic mail addresses
  • Social Security numbers
  • Medical record numbers
  • Health plan beneficiary numbers
  • Account numbers
  • Certificate/license numbers
  • Vehicle identifiers and serial numbers, including license plate numbers
  • Device identifiers and serial numbers
  • Web Universal Resource Locators (URLs)
  • Internet Protocol (IP) address numbers
  • Biometric identifiers, including finger and voice prints
  • Full face photographic images and any comparable images
  • Any other unique identifying number, characteristic, or code (note this does not mean the unique code assigned by the investigator to code the data

Department of Physiology, Northwestern University

303 E. Chicago Ave, Chicago IL 60611-3008

Phone: (312)503-0404 Fax: (312)503-5101