[Mrtrix-discussion] Problem converting DICOMS with mrconvert

[Donald Tournier]

Hi Todd,

That's an odd problem, I've never come across that before. Not sure where
the problem is, but maybe we can figure it out with a bit more info. Judging
from the sequence names, this is using the Siemens product sequence? Can you
confirm that the acquisition matrix was indeed 128x127 on the scanner?
Sounds like an odd (as in strange :) number to me. One other thing you could
do is run 'read_dicom -all -csa FILE' on an individual DICOM file from the
relevant series. I appreciate this not always easy to do, since the DICOM
standard pretty much states that filenames should be meaningless... If
you're struggling with that, this little command might help:

$ find /home/todd/CF002dicom/ -type f -print -exec dicom_filename -q {} \;

This will print the name of every file in the folder hierarchy, followed by
a more readily interpreted filename suggestion if it is DICOM. That should
allow you find at least one relevant file to run 'read_dicom' on, and post
the results (make sure you remove all patient-specific information first
though).

Cheers,

Donald.



On 13 July 2011 16:26, Todd Jolly <todd.jolly at uon.edu.au> wrote:

>  Hi all,
> I have been having trouble converting my DICOM files to .mif format using
> mrconvert. Once the DICOM series has been read, an error comes up saying
> that the acquisition matrix [ 128 127 ] does not fit into the DICOM mosaic.
> I was wondering if anyone else has come across this problem and if there is
> a way around it? The error is shown below.
> Thank you in advance
> Todd
>
> todd-Precision-T1500:~> mrconvert /home/todd/CF002dicom/ dwi.mif
> mrconvert: scanning DICOM folder "/home/todd/CF002dicom/"  - ok
> Select series ('q' to abort):
>    0 -    3 MR images 10:25:25 localizer (fl2d1) [1]
>    1 -  176 MR images 10:29:54 T1_Sag_iso_ASRB (tfl3d1_ns) [2]
>    2 -   65 MR images 10:46:33 ep2d_diff_mddw_55 slice_64 directions
> (ep_b3000#34) [11]
>    3 -   55 MR images 10:58:21 ep2d_diff_mddw_55 slice_64 directions_ADC
> (ep_b0_3000) [12]
>    4 -   55 MR images 10:58:22 ep2d_diff_mddw_55 slice_64 directions_TRACEW
> (ep_b3000t) [13]
>    5 -   55 MR images 10:58:22 ep2d_diff_mddw_55 slice_64 directions_EXP
> (ep_b3000) [14]
>    6 -   55 MR images 10:58:22 ep2d_diff_mddw_55 slice_64 directions_FA
> (ep_b0_3000) [15]
>    7 -   55 MR images 10:58:22 ep2d_diff_mddw_55 slice_64 directions_ColFA
> (?) [16]
> ? 2
> mrconvert: reading DICOM series "ep2d_diff_mddw_55 slice_64 directions"...
> 100%
> mrconvert: acquisition matrix [ 128 127 ] does not fit into DICOM mosaic [
> 1024 1024 ] in image "CF002 (CF002) [MR] ep2d_diff_mddw_55 slice_64
> directions"
> mrconvert: error opening image "/home/todd/CF002dicom/"
>
>
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>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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