Tips and Tools for the FMRI Lab

( Most of this stuff is for internal use only and will probably not work for you if you are not in our lab. ) 

In this page:

Transferring Pfiles   | Transferring reconstructed images (from GE database) | Sample Poster for ISMRM | Scanner Quirks | Scanner Operation Notes | Software | The standard Processing Stream | Useful Documents | Notes for the 2 coil ASL system |  Reconstructing standard images yourself

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Please send MAIL to contribute to this page
 Page maintained by Luis Hernandez-Garcia.

 

Transferring Pfiles: 

use the following scripts to download P files from the scanner:

/optnet/bin/listraw    (shows a list of Pfiles on the scanner)
/optnet/bin/getraw    (does the actual file transfer)

Raw data from standard GE sequences also gets saved as Pfiles but only if the following CV was set during acquisition:  

rhexecctrl = 1

The file contains a header followed by a long string of complex int16 numbers  (ie - real-imaginary-real-imaginary ...) in the order in which they were acquired.  Warning: in a 3D acquisition, the scanner does the FFT along the slice direction if rhexecctrl is not right.

Transferring reconstructed images (from GE database):

 

You need to get on the actual console for this.  On a Shell, do this:  

> cd /usr/g/insite/tmp

> list_select_ex

 

(this is a menu driven program that browses through  the data base.  To  extract the files, do

 

a  exam_number   b series_number    c first_image  last_image
 

quit the program with "Q"

tar the files into a single file

 

> tar cvf subject.tar e????s*

 

Back on your machine you can ftp them or run the programs:

 

listcooked

getcooked

  

Sample Poster for ISMRM : 

 Here

 

Scanner Quirks: 

 Here

 

Scanner Operation Notes: 

 Here

 

Software:

 Luis' shared stuff (interpsinc, interp_asl, orthov m-files stuff ...)

... others?

 

The statndard Processing Stream: 

 Here

 

Useful Documents:

 Unix reference notes by Alberto and Luis

Doug's MRI primer

 

Safety Screening form

Non - employee payment forms

Employee payment forms  (please fill out the dept, contact person, phone# and amount before giving it to Eve.)

   

 

Notes for the 2 coil ASL system :

Here

HIPAA (new) Consent form for ASL studies

Reconstructing images from standard GE sequences yourself

Setting  rhexecctrl = 11 during prescription, determines that a Pfile should be saved to

/usr/g/mrraw/

That P file has the complex k-space data.Brad has a pfile reader for spgr files in

/net/waters/data/bpsutton/Data/Bubble/preadspgr.m

The recon file for spgr is also in that directory, recon_spgr.m.  NOTE:
gspxx will not recon non-spiral images. 
If you image in 3D mode, the z-direction FFT is already done for you by the scanner.  Don't ask why