[Mrtrix-discussion] Problem converting DICOMS with mrconvert

[Donald Tournier]

Hi Todd,

Yes, this is pretty strange. I thought I had Siemens mosaic format figured
out, but maybe I don't... In any case, there doesn't seem to be any
information in the CSA headers about how to handle a case where the mosaic
is not a multiple of the acquired matrix. Since you say the other derived
images are all 128x128, I have to assume that it must divide out the mosaic
evenly into as many chunks as will fit in, but that really is just a guess.
I can propose a fix, which is my best guess as to how to handle this case,
but it really is just a guess - worth a shot though. If this works, I'm
guessing the top or bottom row of the derived images will be padded with
zeros - maybe you can check this?

In any case, the fix is to modify a few lines of code
in lib/file/dicom/mapper.cpp at line 249 from:

          if (image.dim[0] % image.acq_dim[0] || image.dim[1] %
image.acq_dim[1])
            throw Exception ("acquisition matrix [ " + str
(image.acq_dim[0]) + " " + str (image.acq_dim[1])
                + " ] does not fit into DICOM mosaic [ " + str
(image.dim[0]) + " " + str (image.dim[1])
                + " ] in image \"" + H.name + "\"");

to:

          if (image.dim[0] % image.acq_dim[0] || image.dim[1] %
image.acq_dim[1]) {
            error ("WARNING: acquisition matrix [ " + str (image.acq_dim[0])
+ " " + str (image.acq_dim[1])
                + " ] does not fit into DICOM mosaic [ " + str
(image.dim[0]) + " " + str (image.dim[1])
                + " ] in image \"" + H.name + "\" - adjusting matrix size to
suit");
            image.acq_dim[0] = image.dim[0] / guint (float(image.dim[0]) /
float(image.acq_dim[0]));
            image.acq_dim[1] = image.dim[1] / guint (float(image.dim[1]) /
float(image.acq_dim[1]));
          }

Obviously, you'll need to ./build and install again after the change.
Let us know how that works out...
Cheers,

Donald.


On 14 July 2011 14:55, Todd Jolly <todd.jolly at uon.edu.au> wrote:

>  Hi Donald,
> Yes we are using a Siemens Verio 3T. After running 'read_dicom -all -csa'
> it does show that the acquisition matrix is 127p*128... However it does also
> say that there are 1024 rows x 1024 columns?
> Further, if I open up the header on all of the other diffusion DICOM's
> (e.g. ADC, EXP, FA etc) the acquisition matrix is 128x128?
>
> I have attached the information from the header after running 'read_dicom'.
> Many thanks
> Todd
>  ------------------------------
> *From:* Donald Tournier [d.tournier at brain.org.au]
> *Sent:* Thursday, 14 July 2011 11:04 AM
> *To:* Todd Jolly
> *Cc:* mrtrix-discussion at www.nitrc.org
> *Subject:* Re: [Mrtrix-discussion] Problem converting DICOMS with
> mrconvert
>
>  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
>



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