[MINC-users] Segfault in dcm2mnc on PET data from the Siemens mCT

[Jérôme Redouté]

Dear all,
We have the same issue regarding dcm2mnc conversion for PET images 
coming from Siemens mCT scanner.
We tried the following command:

dcmodify -e "(0029,1010)" *.dcm

before to run dcm2minc, but it didn't fix the segfault crash.
Any ideas on what we are doing wrong?
Thanks for your help
Jerome



> We have been using dcm2mnc for many years to convert our Siemens PET
> images to Minc. dcm2mnc is now failing with segfault after a scanner
> upgrade to Siemens newest PET scanner, the mCT PET/CT with TOF. This
> is the case both for minc 2.0 and 2.1.
>
> We have tried to localize the error - dcm2mnc is failing on a private
> tag (0029,1010) not present in older Siemens implementations (VR is OB
> accordint to Siemens Conformance statement) and we get the following:
>
>
> Using dcm2mnc on the new Siemens PET images results in a segmentation
> fault occuring at
> line 487 in acr_io.c:
>
> 485      ptr1 = (char *) input_value;
> 485      ptr2 = (char *) mach_value;
> 486      for (i=0; i<nvals*value_size; i++) {
> 487         ptr2[i] = ptr1[i];
> 488      }
>
> The problem occurs in the acr_parse_siemens_proto2 call after having obtained
> a non-null element in dicom_to_minc.c, line 886:
>
> 886    element = acr_find_group_element(group_list, SPI_Protocol2);
> 887    if (element != NULL) {
> 888        group_list = parse_siemens_proto2(group_list, element);
> 889    }
>
> acr_find_group_element(group_list, SPI_Protocol2) finds the
> (group,element) pair
> corresponding to SPI_Protocol2 (0029,1010) (see spi_element_defs.h). It returns
> an Acr_element if it exists and NULL if it does not.
>
>
> The segmentation fault occurs in the call to
>
>    acr_get_long(ACR_LITTLE_ENDIAN, 1, byte_ptr + byte_pos,&len);
>
> in dicom_to_minc.c:803 during the second iteration of the loop.
> The update in line 813
>
> 813     byte_pos += ((len + 3) / 4) * 4;
>
> causes byte_pos to become very large (overflow?), which may be the
> source of the segfault.
>
>
> A quick fix is to delete the tag (0029,1010) using standard dicom
> tools or f.eks Osirix, Uncommenting of the parse_siemens_proto code
> will also work.
> Any suggestens is welcome, I will be happy to test and can also
> provide testdata to anyone interested into looking into this.
>
> Best regards,
> Flemming
>
> -- 
> Flemming Littrup Andersen, Ph.D
> Rigshospitalet Copenhagen, Dep. PET-3982
> Phone: +45 3545-8143
> Mobile: +45 2615-7368


-- 
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Jérôme Redouté
Ph.D. - Ingénieur de Recherche - Université Claude Bernard - Lyon1
CERMEP - Imagerie du vivant
Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire
59 Bd Pinel
69677 Bron - FRANCE
tel : 33 (0)4 72 68 86 13 (bureau)
tel : 33 (0)4 72 68 86 00 (standard)
fax : 33 (0)4 72 68 86 10
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