aguirreg

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 '$' will be used to indicate a shell command (what is to be typed in the terminal window) and brackets([]) will be used to indicate when you are to insert text of your own described by text within the brackets.

1. $cp /media/[CD title]/[folder(s)]/* .
   • e.g. “cp /media/FFF/11071553/* .” - identifies one folder and copies all files within the folder to the current directory
   • e.g. “cp /media/FFF/1107*/* .” - identifies all folders beginning with 1107 and copies all files within them to the current directory (it may be important to note here that all folders created on CDs will begin with the month and day. Therefore, the example folders were created on November 7th. This is a handy way to make sure you copy all folders on the CD at once).
   • Be sure to copy ALL raw data from all folders on the CD before ejecting and continuing on. CDs always contain one folder, but may contain more than 1.
   • Dicomdir files do NOT need to be copied

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:

  vbrename SUBJECTID 

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:

1. Localizer (ends in “_localizer”
2. MPRage (typically end in “t1_mpr_AX_MPRAGE” or something similar (always with MPRAGE in it))
3. several BOLD scans (typically have “ep2d” and a number of TRs in the name, e.g. “0100_ep2d__pace_150”)
4. Single EPI image (it is preferred that this is acquired, but not guaranteed

Other types of files may include, but are not limited to:

1. DTI scans (can include “psc” in the name)
2. Perfusion scans (generally have “fairest” in the name)
3. CASL scans (incluse “casl” in the name)

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.