[Mrtrix-discussion] GE diffusion data

[Donald Tournier]

Hi Michael,

Yes, I'd made a few changes to support (some) GE DICOM files, but GE's
convention for storing their gradient orientations keeps changing depending
on the software version. I'd only coded support for their latest release (I
think). Not surprising that it doesn't work for everyone...

Happy to have a look into it if you send me the data. The other option is
for you to send me just a dump of the DICOM headers: it's often possible to
have a guess as to which entries are important just by having a look at the
headers...

You can do dump the headers by running the following little script on your
DICOM files, and sending me the output file "dicom_headers.txt.gz". Just
make sure you set the /path/to/dicom/files and SeriesNumber to the correct
values, and copy/paste into a terminal (I assume you use the BASH shell?).
If you know you only have one series (your DW data) in your data folder, you
can remove the first 'read_dicom' line. Otherwise, to figure out the correct
SeriesNumber, run mrinfo /path/to/dicom/files: the series number is the last
entry in square brackets in the series listing.

( cd /path/to/dicom/files
for name in *; do
read_dicom -all $name | grep -aq 'SeriesNumber.* 3 ' &&
(
echo ==============================
echo $name
echo =============================
read_dicom -all $name
);
done ) | gzip > dicom_header.txt.gz

Cheers,

Donald.


On 14 July 2010 06:22, Michael Zeineh <mmzeineh at gmail.com> wrote:

> There was a post regarding incorporating GE diffusion data in October.
> Just curious if there is any update. I have diffusion data of which
> dcm2nii can read the directions (albeit painfully oriented
> incorrectly), but mrconvert gives a "no dicom images found error" on.
> Happy to email the anonymized dicom file.
>
> Michael
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>



-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20100714/0583fda1/attachment.html