fMRI Primer

05 Retreiving Data from the Scanner


If your data was acquired after May 2006 and you will be using SPM.

1. Go to the Apple Mac at the back of the lab outside Ray’s office
2. Show the database window
3. Click on the ‘research’ database in OSIRIX.
4. Single-click (don’t double-click!) your study
OSIRIX database facility, export is in the top toolbar

5. Select your study and click on export, save in /XDATA/dicom_export/research/
6. It is possible you have an entire folder for all your studies, one level below research
7. Once it is done downloading, take these simple steps to save yourself time down the road:
a. Navigate to your folder
b. double click it. You will see that inside are all your functional runs, your SPGR, inside a folder that is, well, inside your folder. In other words a pointless layer of foldering between your data and you. This folder is a problem that you want to eliminate
c. Move the functional runs and SPGR up one level
d. Delete the now empty folder
e. Ensure all your file names have no spaces in them, only underscores and dashes
f. WRITE DOWN the full name of each file. For example, your study PETBRV222 may have an absurd string on the end – LEJL85. Write this down, it helps to know it.
g. Now go back to your favorite Nimbus workstation


Dialogue box showing location of exported research studies

8. Now login to nimbus (SUN/PC/Apple)
9. cd /export/data/scanner/
10. To copy over your images from ‘lights’ to ‘nimbus’ to work on type the following all on one line
scp –r .
and type in your apple password when asked for it. Note the words in italics should be replaced by your OWN subject ID and study ID. NOTE SPACE BEFORE THE PERIOD AT THE END!!!!

PLEASE NOTE: what –r means is ‘recursive’ which means it will do this to every folder in the folder, including every individual subject.

If using SPM or FSL, make sure you are on nimbus, and then:
11. Type imagej & at the prompt to open up the dicom convertor.


12. Select Plugins/import dicom sequence
13. Navigate, in the Folders window, to export/data/scanner/yourfile
14. Note that if you have a folder with multiple runs, you need to navigate to the first run in the first folder, etc.
15. Select the first *.dcm file in the /export/data/scanner/studyID/ directory and click OK then click OK on the Sequence options boximage-4.jpg

Note that each of your functional acquisitions are in a directory called EPI BOLD # REPS and that the total # of images = # of slices x # of volumes.

16. After all the images in the run have been opened select image/properties and put # of slices in Depth (z) box and # of acquisition volumes in Frames (Time points) box and click ok. If you know the number of volumes you acquired, you can calculate the number of slices simply by dividing the number of frames by the number of volumes acquired. For example if you acuired 10 volumes of 20 slices this will create 200 images.


17. Select File/saveas ANALYZE7.5 in the /data/study/studyID/ as r#.img. It will show that it is running through and saving all of these. PLEASE REALIZE YOU NEED TO ENSURE YOU ARE SAVING THIS TO THE FOLDER YOU WANT IT IN!!!
18. Iteratively repeat this sequence for all of the runs in your study(s),


Remember that you will have to create this directory before hand.

Now these files are ready for FSL. You need to copy them over. Realize that you are currently on Volumes/Clinical/scanner/yourfile and you want to go to Volumes/Clinical/analyzed/yourstudy

so type:

cp yourfile ../../../analyzed/yourstudy and whatever string follows

Now you are ready to preprocess!

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