Dear BIRN developers,

first of all, thanks a lot for providing the tools for the QA.

We have a minor issue for the fmri_phantom_qa.pl routine (included in bxh_xcede_tools-1.11.1-lsb30.x86_64). The routine works without any problems and produces the expected html report. However, we would like to have more information about the exact location of the ROI and ghost masks. Is it possible to have an output file for the internally created ROI and ghost mask (similar to the left figure of the attached file)? I had a look into the manual and found these informations:

For EPI sequences, this image plots the
"ghostiness" of the data. The ghost metric is
calculated for each volume by calculating a
dilated mask ("original mask") of the motion corrected,
detrended data, and shifting it by
N/2 voxels in the appropriate axis to create a
"ghost mask". The mean intensities of those
voxels in the original mask and not in the
ghost mask, and of voxels in the ghost mask
and not in the original mask are calculated.
The mean intensity of the top 10 percent
of ghost-only voxels ("meanBrightGhost")
is also calculated. The ghost values are
plotted as a percentage of the mean intensity
of non-ghost voxels. The dilated mask is
generated using the following sequence of
AFNI commands:
3dvolreg --prefix REG INPUT
3dDetrend --polort 2 --prefix
DETREND REG
3dTstat --mean --prefix MEAN REG
3dAutomask --q --dilate 4 --prefix
MASK MEAN

Based on these informations, I tried to reproduce the ghost mask (see right figure of the attached file), by shifting the dilated mask by N/2 voxels (half of the FOV). The resulting ghost mask has substantial overlap with the phantom for our dimensions (spherical phantom diameter: 165 mm ; FOV: 220 mm; Matrix: 64x64). Is this the expected location for the ghost mask or did I misunderstand something? Are there any alternatives or recommendations for creating/confirming the position of the ROI and ghost mask?

Best Regards

Sebastian Höfle
D'Or Institute for Research and Education (IDOR)
Phone/Fax: +55 21 3883 6000
e-mail: sebastian.hoefle@idor.org
http://www.idor.org