> Thank you very much for the reply. I'm sure you're sick of answering the
> same orientation questions.
Take a look at this link and see what you think...
http://www.jiscmail.ac.uk/cgi-bin/webadmin?S2=SPM&m=22637&f=john%40fil&q=flip+and+left+and+right
> I understand that the obvious best solution is to convert from dicom to
> nifti, but for the here and now, I just want a little understanding of how
> this setting comes into play.
Its simple really. If an image does not have its orientation explicitly
specified in its .hdr or .mat file, then SPM5 can only determine this
information elsewhere. Therefore it checks by looking at the defaults.
Any images that are created or any headers that are modified will be written
in NIfTI format. In this format, the handedness is explicitly stated in the
header. If you provide an image where the orientation needs to be determined
by the flip setting, then any images that are derived from this image (or any
modifications to its header) will explicitly encode this orientation in the
new header.
If the orientation of the original image is correct, then subsequently
generated images will have the correct orientation.
If the orientation of the original image is wrong, then subsequently generated
images will have the wrong orientation.
> On a similar note, when I converted the
> entire scan (5500 images for an 11 min., TR= 3 session) to a single .nii
> file, using mri_convert again, SPM5 wouldn't let me slice-time. Is this a
> bug, or do I need separate files for each volume (i.e. image001 -
> image219)?
SPM has problems with very large files.
> I would love to use SPM to convert the DICOM's, but as of now
> it's been running for over an hour, whereas mri_convert does it in a couple
> minutes :-/ Any tips on how to speed things up (mri_convert is a pure C
> program, and, as I understand it, Matlab doesn't handle 5500 file I/O's as
> quickly).
Just convert about 1000 dicom files at a time. The reason for the slowness is
that SPM reads and saves all the header information before trying to convert
the images. These headers (particularly those of Siemens fMRI data) require
an enormous amount of memory. I have fixed this memory issue for the
forthcoming SPM version, but not for SPM5.
There are also a bunch of other dicom to NIfTI converters that you could try.
A search of http://idoimaging.com/index.shtml would be a good place to start.
Best regards,
-John
|