This is the Auxillary Center for Functional Neuroimaging (CfN) Website

(The main CfN website can be accessed at cfn.upenn.edu)

 

Siemens saves their multi-slice EPI images in Mosaic format,meaning the slices from one volume are tiled into one 2D image.

Example EP2D_BOLD images in Mosaic form.

The number of slices obtainable with the Siemens EPI BOLD sequence is significantly greater than the GE limits. Here are the slice number limits for different TR and TE values.

TR (ms)
TE (ms)
Max Slices
1500
30
23
2000
30
31
3000
30
45
4000
30
62
1500
40
20
2000
40
27
3000
40
40
4000
40
54
1500
50
17
2000
50
23
3000
50
35
4000
50
57

 

Help Yourself to the Following:

1. Example Siemens fMRI image files from a BOLD EPI experiment (done on HUP5 03/05/2003).

These are Dicom images in Mosaic format: Download Dicom images (gzipped tar file)

Here's a first attempt at converting the same images to ANALYZE format: Download ANALYZE images (gzipped tar file)

2. Siemens documentation on synchronizing to the MRI sequence using gating signals.

Download the PDF file.

3. Finger tapping fMRI: T1-weighted structural and EPI images (done on HUP5 03/17/2003).

fMRI paradigm: Left hand finger-tapping, TR=2sec, 10 TR epochs w/ 2sec finger-tap at start of each epoch, 240 total images (realreps), 24 epochs.

Image # 1 2 3 4 5 6 7 8 9 10 11 12 13 14
Event tap rest rest rest rest rest rest rest rest rest tap rest rest rest

 

and so on ...

Download the T1 images (dicom format) Download the EPI images (Mosaic dicom format)

Download the T1 images (ANALYZE format) Download the EPI images (ANALYZE format)

4. View the Siemens description of their image file Dicom header fields.

5. 3D MPRAGE image acquired on the 3T (1x1x1 mm voxels, 160 slices, 5:14 acquisition). Download ANALYZE format image.

6. 3D SPGR image acquired on the 3T (1x1x1 mm voxels, 176 slices, 6:20 acquisition). Download ANALYZE format image.

7. Compare MPRAGE images from the 3T with different TI times (1100ms vs. 950ms). Download ANALYZE format images.

8. View the directions for the HUP 5/6 Projection Setup for fMRI Experiments.

9. More comparison data of SPGR (Siemens vs. GE protocols) and MPRAGE (TI=900 & 1100 ms), from the 3T. Download ANALYZE format images.

10. A script to read the Siemens MOCO parameters from the Dicom "shadow" header. Download the script and DLLs (compressed tar file).

After download: run the Csh script "get_moco" on a Linux system with Wine installed.

11. Manual to use the Siemens Physiologic Monitoring Unit (PMU). Download PMU.doc.

 

for questions regarding this page, contact Mark Elliott