Downloading CRTC Data

Our fMRI data is typically posted to the CTRC Owncloud website within one or two days after acquisition (possibly longer if the scan was a Friday). These directions assume that you have the URL and login/password to access the Owncloud website.

Identify the Subjects

Internally, we use our own set of Subject IDs, which are generated when a participant enters our experiment. The CTRC does the same thing, meaning that our subject numbers do not line up with those at the CTRC. Moreover, the same participant scanned multiple times will have a new CTRC subject number for each scan. It is imperative that you be able to translate between our subject numbers and those assigned to the fMRI data by the CTRC!

The timestamps for each zipped data set are visible through the Owncloud interface. As a rule of thumb, the most recently acquired data will also be the one with the most recent timestamp. If there is really only one candidate file, it should be fairly easy to identify the files you want. If you need to download older data, or if there are multiple candidates, you can consult the fMRI Log File Google Spreadsheet, which lists the CTRC subject number along with our own internal subject number.

Download the Data

Each fMRI session has two associated zip files. You can ignore the ones labeled study_files, as those are stored in a proprietary data format and are useless to us. Instead, you will want to download the NIFTI files to your local hard drive.

File Organization

Once the download has finished, you can unzip the files to a local directory. The CTRC assigns sequential numbers and other file information to each of these files, and so we generally rename them according to our NIFTI file organization and naming convention.

An important step here is to check whether all expected files are present. We are generally expecting to see the following key files:

1. A file with MPRAGE appearing somewhere in the filename. This is the high-resolution (~1mm voxels) anatomical image. It will likely begin with the prefix 500 or 501, and should be roughly 20MB in size.
   • Create a subdirectory called mri and move this file to the new subfolder, renaming it to MPRAGE.nii
2. A set of files with BOLD appearing somewhere in the filename. These files may be prefixed with numbers in the range of 700, 800, 900, etc..
   • These are the most likely to be problematic because sometimes a run will have to be aborted (e.g., the experiment malfunctioned) meaning there will be some dud files.
   • These files should be somewhere in the range of 50MB
   • There should be exactly one of these files for each run that the participant completed. If there are extra files, it is likely that a run was restarted. If there are fewer, this is more troubling, since that means we are missing some data, and this needs to be followed up on with the CTRC (it also makes it ambiguous which runs have missing data)
   • Our LDT and Semantic Imagery experiment have 6 runs. If we have 6 full runs, all is good in the hood.
   • If you are confident that you know that the data are complete, go ahead and create a directory called bold. Under that directory, create run directories called 001, 002, ... etc. (one for each run). Move each of the BOLD files to these run directories, and rename to f.nii.gz
3. The scan session may include a T2- or FLAIR image, which helps identify gray matter. The unzipped files may include a file with FLAIR or 3D_T2 in the name. Expect a FLAIR file to be approximately 20MB, and the 3D_T2 file to be over 100MB in sise.
   • If these files exist, copy them to the /mri subdirectory you created in Step 1