Thanks so much for your detailed help.  When I run the analysis in FEAT
it actually doesn't rotate the EPI image, I just get a horrible
registration result and my data is shown upsidedown. So what I've been
doing from the beginning (apparenty correctly by accident!) is flipping
my highres anatomical and MNI images using ImageJ and using those
flipped brains for the analysis.  So assuming that the flipped brains
started out in radiological convention (RPI) then my final result or
anatomical and functional is in RAI and everything is lined up.

Can you confirm if the MNI and if a MPRAGE done on a GE scanner come
out in RPI or LPI formats?

Andy


On Saturday, January 25, 2003, at 08:50  PM, Jim Murakami wrote:

> Andy,
>     The problem is with the GE to Analyze step.   Each GE image (when
> extracted from the scanner using ximg for older scanners or the Image
> Export function in RTIP for those using this platform) are stored in a
> file format such that there is a header and then the Data.   The data
> is
> inverted top to bottom during the step from the scanner to the file you
> export to your workstation for processing.
>     For instance, if you started with an axial image of the head on a
> GE
> scanner.   At the scanner console you would be looking at it with the
> medical/radiological convention (right side of the head on the left of
> the image, left side of the head on the right side of the image,
> anterior
> part of the head at the top of the image, and posterior part of the
> head
> at the bottom of the image).
>     When you ask the scanner to extract the image from the database on
> the scanner is writes the data into a file called I.001 or
> E####S###I1.MR    This is the file which sits in the Unix directory on
> the scanner computer that you then tar and ftp to your workstation.
> This file is written such that there is a header and then a file
> containing 256x256 (or 64x64) 16 bit ints.    Here is the goofy part.
> The first line of data is actually the line from the BOTTOM of the
> image
> and not the top.   The last line of ints is the line from the TOP of
> the
> image.    SO, if you just skip the header and read the data into an
> image
> file and then look at it.   The image will be inverted (not rotated)
> top
> to bottom relative to the image you saw on the GE console.    If you
> view
> this image in "slices" you will see the image inverted top to bottom
> (anterior part of head on the bottom, posterior part of head on top,
> left
> side of head on the right of the image, and right side of the head on
> the
> left of the image).   THIS IS THE IMPORTANT PART.    When you read the
> 4d
> Analyze data set into FSL (not sure what happens in AFNI) it gets read
> in
> this way.   That is why slices and the FEAT report.html files show the
> person looking at the bottom of the image.    This in and of itself is
> ok, if you remember which side of the image is which.
>     Here comes the bad part.    When you register the data set with the
> Standard brain in FSL (which has the brain looking "up" in the picture
> (if viewed in slices and by FSL)  FSL ROTATES the image 180 degrees to
> match up with the Standard brain.   It does not invert the image, but
> rotates it.   Therefore, the functional data set gets displayed in LPI
> format on top of the standard brain which is in medical format.  (The
> two
> data sets are inverted right to left relative to each other).
>     One must be very careful about which side of the head is which when
> working with these GE files.    I would advise people to run a 3D data
> set on an asymmetric phantom.   Pump it through your GE to Analyze
> conversion scripts.   And see which side of the image is left and right
> before and after pumping it through FSL or AFNI.
>     Jim
>
> Andy Goldfine wrote:
>
>> I didn't realize this wasn't normal until these past few threads, but
>> the results of every one of my FEAT runs has the y-axis in anterior to
>> posterior.  When I look at the data before running FEAT using to3d
>> (from AFNI) it's all in LPI format.  [FYI, my original data is
>> converted from GE to Analyze by an internal program called adw24d and
>> then I need to create a .hdr using avwcreatehd since adw24d creates a
>> .hdrs and a .img.]  Does this happen to anyone else?  What am I doing
>> wrong?
>>
>> Thanks