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Data Transfer; Cleaning Up
Data Management: moving anatomies and Pfiles to local drives
There are separate instructions for anatomicals and functions. The reason is that anatomicals are created on a separate computer from the functionals.
Checking that you have enough disk space:
Prior to starting, you should have made sure you have enough disk space on your local drive partition.
You will get an output like this:
>> ssh moach -l username [e.g., 'sayres']
password: >> [enter your password]
>> cd /biac2/kgs/mri/ 11
>> df -h .
In this case, Avail=24G, so we have 24 Gigs of free space. There should be at least 4 Gigs of free space, or you're in trouble. (Realistically, a session will take up 1-2 Gigs of space usually, but it's important to leave some buffer space on the RAID.)
Filesystem Size Used Avail Use% Mounted on biac1:/u3/kgs 806G 741G 24G 97% /biac1/kgs
'Push'-ing to Lucas-DICOM3T
The setup for transfer has changed recently. Files are transferred from the control computer to the Windows box just outside the scanner, Lucas-DICOM3T. You use 'get11' to get the anatomicals (now in DICOM format) and SecureFX (sftp) to transfer Pfiles over. You can also use this to transfer everything from Lucas-DICOM3T to the RAID. Follow the instructions Anne provided in this PDF (should be also on the side of the machine):
We have a folder in the 'Image Data' directory: Grill-Spector lab. Transfer the data there. Then from there, you can make a link to moach, and copy to the RAID.
Some tools for after tranferring
We have a few linux tools and matlab scripts for setting things up after you've transferred your data. This code should be in /biac1/kgs/dataTools/.
dcm2gen -- linux code to convert DICOM files to GENESIS I-files.
Type 'dcm2gen *' to convert all files in a directory.
writeihdr -- linux code to write an E-file header from a P*.7 file.
grecons -- linux code to write a P*.mag file from a P*.7 file
Usage: Type 'grecons -b -O P[#####].7' to recon a file
These scripts will call the above files from MATLAB, to make things easier:
SetupRawDir -- if you've dumped all your anatomicals and Pfiles, and want to set up the old Raw directory, like w/ simptrans3.sh. There is a flag to create I-files from DICOM for all anatomicals, at the same time.
ReconOffline -- automatically recon (make Pmags and Efiles) all files in the current directory, or in Raw/Pfiles.
Last modified 2004-Jun-8 05:28 GMT.