Siemens mosaic diffusion scan upside down (and solution)

[jpcoutu]

We have a dicom series for which the scan was flipped upside down. The mosaic has a clear transverse orientation (as observed with xmedcon), but this bit of code went wrong (in parse_siemens_proto2 in dicom_to_minc.c) and determined the mosaic has coronal orientation, because the direction cosine along z was -0.99, and absolute values are not used when doing comparisons:

        else if (!strcmp(name, "SliceNormalVector")) {
            if (vm == 3 && n_values >= vm) {
                Acr_Double tmp[3];
                Acr_Short orientation;

                tmp[0] = atof(value[0]);
                tmp[1] = atof(value[1]);
                tmp[2] = atof(value[2]);

                orientation = TRANSVERSE;
                if (tmp[0] > tmp[2] && tmp[0] > tmp[1]) {
                  orientation = SAGITTAL;
                }
                else if (tmp[1] > tmp[2] && tmp[1] > tmp[0]) {
                  orientation = CORONAL;
                }
                acr_insert_numeric(&group_list, EXT_Slice_orientation,
                                   orientation);
            }
        }

The solution was simply to change to tmp[i] = fabs(atof(value[i])) for the values in the tmp array. The downstream effect with the orientation being set wrong is that EXT_Slice_inverted does not get set to 1 in add_siemens_info as it should when sSliceArray.ucImageNumbTra is 1, resulting in the flip:

        temp = acr_find_int(group_list, EXT_Slice_orientation, -1);
        prot_find_string(protocol, "sSliceArray.ucImageNumbTra", str_buf);
        if (str_buf[0] != '\0') {
          if (temp == TRANSVERSE && strtol(str_buf, NULL, 0) == 1) {
            acr_insert_string(&group_list, EXT_Slice_inverted, "1");
          }
        }

[vfonov]

@rdvincent ?

[jpcoutu]

This is fixed in https://github.com/BIC-MNI/minc-tools/pull/113