<div>Hi all,</div>
<div> </div>
<div>I originally have a dicom series of 2d slices which I had converted to a 3D dicom volume for processing.</div>
<div>I'll try processing the dicom series and then write the output to a dicom series of 2d slices, to see if I can circumvent this problem.</div>
<div>I'll let you know if this works?</div>
<div> </div>
<div>I'll provide a link to my data as well, but it probably won't be until the weekend.</div>
<div> </div>
<div>Thanks,</div>
<div>john<br><br></div>
<div class="gmail_quote">On Fri, Nov 27, 2009 at 12:23 PM, Mathieu Malaterre <span dir="ltr"><<a href="mailto:mathieu.malaterre@gmail.com">mathieu.malaterre@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">This is a post ITK 3.16 feature I am afraid:<br><br><a href="http://www.cmake.org/Bug/view.php?id=7748" target="_blank">http://www.cmake.org/Bug/view.php?id=7748</a><br>
<br>(0017626)<br>Mathieu.Malaterre (developer)<br>2009-09-19 06:51<br><br> This will be post ITK 3.16.<br><br>Thanks for the patch ! Sorry for being so long to fix it.<br>
<div>
<div></div>
<div class="h5"><br>On Fri, Nov 27, 2009 at 6:11 PM, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>> wrote:<br>> John,<br>><br>> 3.16 will not help. This looks like a bug for sure.<br>
><br>> Can you provide a link to a dataset that we can use to reproduce the<br>> problem? We don't have much experience with 3D dicom files I'm afraid.<br>><br>> Bill<br>><br>> On Fri, Nov 27, 2009 at 11:59 AM, John Drozd <<a href="mailto:john.drozd@gmail.com">john.drozd@gmail.com</a>> wrote:<br>
>> Hi Bill,<br>>><br>>> I am currently using the ITK 3.14 that is in the 3D Slicer 3.4<br>>> directory Slicer3-lib/Insight<br>>><br>>> If I upgrade to ITK 3.16, will this solve my problem?<br>
>><br>>> I downloaded ITK 3.16 and noticed using the diff command that<br>>> itkGDCMIO.h has been modified from what it was in ITK 3.14.<br>>><br>>> But when I ran diff on gdcmOrientation.cxx in both versions of ITK,<br>
>> diff showed no difference.<br>>><br>>> John<br>>><br>>> On Friday, November 27, 2009, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>> wrote:<br>>>> John,<br>
>>><br>>>> What version of itk are you using? Are you using the gdcm 1.x that is<br>>>> in the itk source tree or an external gdcm 2.x version?<br>>>><br>>>> Bill<br>>>><br>
>>> On Thu, Nov 26, 2009 at 3:22 PM, John Drozd <<a href="mailto:john.drozd@gmail.com">john.drozd@gmail.com</a>> wrote:<br>>>>> Hi Luis,<br>>>>><br>>>>> I was getting a segmentation fault because I had forgotten to change the<br>
>>>> Dimension from 2 to 3 in DicomReadPrintTag.cxx.<br>>>>><br>>>>> For the input image, I have:<br>>>>> (0020|0037) Image Orientation (Patient) = 0.0\0.0\-1.0\0.0\1.0\0.0<br>
>>>><br>>>>> For the output image, I have:<br>>>>> (0020|0037) Image Orientation (Patient) =<br>>>>> 0.000000\0.000000\1.000000\0.000000\1.000000\0.000000<br>>>>><br>
>>>> There is a difference. Since the program is changing the orientation when<br>>>>> processed through the pipeline, is the best approach to manually change the<br>>>>> orientation tag of the dictionary and then copy the revised dictionary to<br>
>>>> the output file?<br>>>>><br>>>>> john<br>>>>><br>>>>> Below are the full tags:<br>>>>><br>>>>> [jdrozd@trumpet DicomImageReadPrintTags]$ ./DicomImageReadPrintTags<br>
>>>> correctedsubject5.dcm<br>>>>> (0002|0000) Group Length =<br>>>>> 214<br>>>>> (0002|0001) File Meta Information Version =<br>>>>> AAE=<br>>>>> (0002|0002) Media Storage SOP Class UID =<br>
>>>> 1.2.840.10008.5.1.4.1.1.2<br>>>>> (0002|0003) Media Storage SOP Instance UID =<br>>>>> 1.2.826.0.1.3680043.2.1125.1.10607669833050788267094246636093811<br>>>>> (0002|0010) Transfer Syntax UID =<br>
>>>> 1.2.840.10008.1.2.1<br>>>>> (0002|0012) Implementation Class UID =<br>>>>> 147.144.143.155<br>>>>> (0002|0013) Implementation Version Name = ITK/GDCM<br>>>>> 1.2.4<br>
>>>> (0002|0016) Source Application Entity Title =<br>>>>> NOTSPECIFIED<br>>>>> (0008|0008) Image Type =<br>>>>> DERIVED\PRIMARY<br>>>>> (0008|0012) Instance Creation Date =<br>
>>>> 20091029<br>>>>> (0008|0013) Instance Creation Time =<br>>>>> 135224<br>>>>> (0008|0016) SOP Class UID =<br>>>>> 1.2.840.10008.5.1.4.1.1.2<br>>>>> (0008|0018) SOP Instance UID =<br>
>>>> 1.2.826.0.1.3680043.2.1125.1.10607669833050788267094246636093811<br>>>>> (0008|0020) Study Date =<br>>>>> 20081030<br>>>>> (0008|0030) Study Time =<br>>>>> 164348.940<br>
>>>> (0008|0050) Accession Number<br>>>>> =<br>>>>> (0008|0060) Modality =<br>>>>> CT<br>>>>> (0008|0064) Conversion Type =<br>>>>> WSD<br>>>>> (0008|0070) Manufacturer =<br>
>>>> Manifacturer<br>>>>> (0008|0080) Institution Name = GDCM<br>>>>> Hospital<br>>>>> (0008|0090) Referring Physician's Name = Refering<br>>>>> Phisician<br>
>>>> (0010|0010) Patient's Name = Patient<br>>>>> 188858520<br>>>>> (0010|0020) Patient ID =<br>>>>> 1747233212<br>>>>> (0010|0030) Patient's Birth Date =<br>
>>>> 19500101<br>>>>> (0010|0040) Patient's Sex =<br>>>>> M<br>>>>> (0018|0088) Spacing Between Slices =<br>>>>> 1.207500<br>>>>> (0018|1164) Imager Pixel Spacing =<br>
>>>> 0.945750\0.945750<br>>>>> (0020|000d) Study Instance UID =<br>>>>> 1.2.826.0.1.3680043.2.1125.1.53653479342656887425609263146205769<br>>>>> (0020|000e) Series Instance UID =<br>
>>>> 1.2.826.0.1.3680043.2.1125.1.47155241092896696198844159625679986<br>>>>> (0020|0010) Study ID =<br>>>>> 1533117581<br>>>>> (0020|0011) Series Number =<br>>>>> 2135500125<br>
>>>> (0020|0013) Instance Number =<br>>>>> 165<br>>>>> (0020|0020) Patient Orientation =<br>>>>> L\P<br>>>>> (0020|0032) Image Position (Patient) =<br>>>>> 199.237496852874\0.0\0.0<br>
>>>> (0020|0037) Image Orientation (Patient) =<br>>>>> 0.0\0.0\-1.0\0.0\1.0\0.0<br>>>>> (0020|4000) Image Comments = NOT FOR CLINICAL<br>>>>> USE<br>>>>> (0028|0002) Samples per Pixel =<br>
>>>> 1<br>>>>> (0028|0004) Photometric Interpretation =<br>>>>> MONOCHROME2<br>>>>> (0028|0008) Number of Frames =<br>>>>> 166<br>>>>> (0028|0010) Rows =<br>
>>>> 256<br>>>>> (0028|0011) Columns =<br>>>>> 256<br>>>>> (0028|0030) Pixel Spacing =<br>>>>> 0.945750\0.945750<br>>>>> (0028|0034) Pixel Aspect Ratio =<br>
>>>> 1\1<br>>>>> (0028|0100) Bits Allocated =<br>>>>> 16<br>>>>> (0028|0101) Bits Stored =<br>>>>> 16<br>>>>> (0028|0102) High Bit =<br>>>>> 15<br>
>>>> (0028|0103) Pixel Representation =<br>>>>> 0<br>>>>> (0028|1052) Rescale Intercept =<br>>>>> 0.0<br>>>>> (0028|1053) Rescale Slope =<br>>>>> 1.0<br>
>>>> (0028|1054) Rescale Type =<br>>>>> US<br>>>>> (7fe0|0000) Group Length =<br>>>>> 21757964<br>>>>> Patient's Name (0010|0010) is: Patient<br>>>>> 188858520<br>
>>>> Performing Physician's Name (0008|1050): (No Value Found in<br>>>>> File)<br>>>>> PixelType:<br>>>>> scalar<br>>>>> Component Type: unsigned_short<br>>>>><br>
>>>> [jdrozd@trumpet DicomImageReadPrintTags]$ ./DicomImageReadPrintTags<br>>>>> outsubject5.dcm<br>>>>> (0002|0000) Group Length =<br>>>>> 194<br>>>>> (0002|00<br>
>><br></div></div>
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