Following scanning of a subject you will receive 1 or more CD(s) with the subject's raw data from the MR techs. The data from these CDs need to be uploaded to the CfN cluster for pre-processing and analysis.
Uploading most often must be done in either the B19 (downstairs) CfN Lab or the Gates (upstairs) CfN Lab.
First, you must be logged into a terminal on the cluster as “iron”. This requires a password. If you are a new member of the lab and need this password please contact Sarah Daina or another member of the lab.
To copy manually
Once you are signed in, select the “Desktop” icon on the Desktop and go into “File Directories.” Manually click the path toward the desired folder into which you want to upload the data (/jet/aguirre…etc). Make a new sub-folder in the project with subject ID.
Insert the CD into the computer and open it when it appears on the Desktop. Copy the raw data files (not dicomdir files) from the CD into the subject ID folder you have made. It may take a while.
Alternatively, you can copy the files over using commands in terminal.
Open Terminal and follow the below commands:
From this point the symbol 'cp /media/[CD title]/[folder(s)]/* .
If you received more than one CD, repeat the above steps 5 - 7 for the remaining CDs.
Once you have copied all of the raw data there will be MANY files within the directory
Again, be sure you have copied ALL of the raw data before continuing on to this step. It will be difficult to tell if you are missing raw images until later in the processing stream.
The raw data files must all be in the same folder to be renamed. In other words, if they copied over in a few subfolders, move them all backwards into the subjectID folder using the command:
mv xxxx* ../
In terminal, and one step back from the folder in which all the raw files are located (in other words, if they are in a subjectID folder, the rename command must be issued in the folder in which the subjectID folder is located)
Type the command:
You are renaming everything contained in the subject ID folder. If everything has been copied correctly this should work smoothly.
If you wish to rename from another directory simply include the path…
For example, if you are in /jet/aguirre
vbrename /[Project Directory]/[SubjectID]
This should give you several types of scan files that all begin with a number that indicates the order of acquisition:
Other types of files may include, but are not limited to:
You are now ready to Pre-process the data. Please continue to the standard_prep-script_and_its_components page for information about setting up/modifying a script to pre-process this data.