SITK::Error - The file has unsupported 3 dimensions

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1

Hello Everyone,

Can you please help me with the below error?

I have a DICOM file which is attached. When we try to convert this into a.mhd file, we get an error as “Teh file in the series has unsupported 3D dimensions”. Can you please help us resolve the issue?

II am also providing the tags information of my file based on code from this link (https://simpleitk.readthedocs.io/en/master/Examples/DicomImagePrintTags/Documentation.html)

(0008|0008) = = “ORIGINAL\PRIMARY\VOLUME\NONE”
(0008|0016) = = “1.2.840.10008.5.1.4.1.1.130”
(0008|0018) = = “2.25.268344867590623757739343791212928671539”
(0008|0020) = = “20190714”
(0008|0023) = = “20190714”
(0008|002a) = = "19700101070000 "
(0008|0030) = = “172248”
(0008|0033) = = “173525”
(0008|0050) = = " "
(0008|0060) = = “PT”
(0008|0070) = = "UNKNOWN "
(0008|0090) = = “”
(0008|1030) = = "UNKNOWN "
(0008|103e) = = "UNKNOWN "
(0008|1090) = = "UNKNOWN "
(0008|9205) = = “MONOCHROME”
(0008|9206) = = “VOLUME”
(0008|9207) = = "VOLUME_RENDER "
(0010|0010) = = “abcd”
(0010|0020) = = “2000”
(0010|0030) = = " "
(0010|0040) = = “Male”
(0018|0050) = = "1 "
(0018|0071) = = “MANU”
(0018|0073) = = “MANU”
(0018|1000) = = "UNKNOWN "
(0018|1020) = = "UNKNOWN "
(0018|1134) = = “STATIC”
(0018|1181) = = “NONE”
(0018|2005) = = "-78-77-76-75-74-73-72-71-70-69-68-67-66-65-64-63-62-61-60-59-58-57-56-55-54-53-52-51-50-49-48-47-46-45-44-43-42-41-40-39-38-37-36-35-34-33-32-31-30-29-28-27-26-25-24-23-22-21-20-19-18-17-16-15-14-13-12-11-10-9-8-7-6-5-4-3-2-1\0\1\2\3\4\5\6\7\8\9\10\11\12\13\14\15\16\17\18\19\20\21\22\23\24\25\26\27\28\29\30\31\32\33\34\35\36\37\38\39\40\41\42\43\44\45\46\47\48\49\50\51\52\53\54\55\56\57\58\59\60\61\62\63\64\65\66\67\68\69\70\71\72\73\74\75\76 "
(0018|9004) = = “RESEARCH”
(0018|9073) = = “0”
(0018|9725) = = “CYLINDRICAL_RING”
(0018|9726) = = “0”
(0018|9727) = = “0”
(0018|9755) = = "FALSE "
(0018|9758) = = “NO”
(0018|9759) = = “NO”
(0018|9760) = = “NO”
(0018|9761) = = “NO”
(0018|9762) = = “NO”
(0018|9763) = = “NO”
(0018|9764) = = “NO”
(0018|9765) = = “NO”
(0018|9766) = = “NO”
(0018|9767) = = “NO”
(0018|9768) = = “NO”
(0020|000d) = = “1.2.826.0.1.3680043.2.1125.4082960453717943603603726631811946355”
(0020|000e) = = “1.2.826.0.1.3680043.2.1125.8397261186222101954520583083004172948”
(0020|0010) = = " "
(0020|0011) = = “”
(0020|0013) = = "0 "
(0020|0032) = = "-120-120-78 "
(0020|0037) = = "0.99999999999999\0\0\0\0.99999999999999\0 "
(0020|0052) = = “2.25.183387019459409372524007875133033107487”
(0020|1040) = = “”
(0028|0002) = = “1”
(0028|0004) = = "MONOCHROME2 "
(0028|0008) = = "155 "
(0028|0010) = = “240”
(0028|0011) = = “240”
(0028|0030) = = "1\1 "
(0028|0100) = = “16”
(0028|0101) = = “16”
(0028|0102) = = “15”
(0028|0103) = = “0”
(0028|0106) = = “0”
(0028|0107) = = “2213”
(0028|0108) = = “0”
(0028|0109) = = “2213”
(0028|0301) = = “NO”
(0028|1050) = = “1106.5”
(0028|1051) = = “2213”
(0028|2110) = = “00”
(0054|0202) = = “STATIONARY”
(0054|1002) = = “EMISSION”
(0054|1210) = = "0 "
(2050|0020) = = “IDENTITY”
Image Size: (240, 240, 155)
Image PixelType: 16-bit unsigned integer

2

These tags were missing earlier and manually added these below tags to this .dcm file by using pydicom

(0010|0010) = = “abcd”
(0010|0020) = = “2000”
(0010|0040) = = “Male”

Can anyone let us know whether there is any issue with our .dcm file? We aren’t able to upload the file. It throws error

3

Please also note that this dicom file was obtained by converting .nii to .dcm form. This data was from BRATS dataset. The shape of .nii file was 240,240,155,4. However I decided to retain only once channel data[:,:,:,0] , so the shape of my DICOM file is [240,240,155]. Hope this info helps

4

How did you convert the nii to dcm? Did you create a series if DICOM files? How are you trying to read your DICOM?

5

Hello,

I tried converting the files using the tools available online. “Nifti to Dicom”/ Mango medical imaging viewer

There was only one dicom file. I didn’t have 155 images.

How do I know the issue is with the DICOM file? I read DICOM file as array

But the shape and everything looks fine. I mean when I use plt.show in Python to view .nii file and .dcm file, they look the same at certain points. I mean [:,:,30] in nii and [:,:,30] in dcm looks the same. I tried this for other slice values as well

Thanks

Selva

6

Can you let us know or direct me to resource where I can actually convert the .nii to .dcm the right way? I am new to all these file formats and your inputs would really be helpful.

Can you help us by sharing details on how to properly convert a .nii to .dcm file?

7

You can try converting it using Slicer, as Slicer has a DICOM writing capability.

8

Hello,

I downloaded slicer and uploaded my .nii file.

To save it as DICOM, I don’t see any option to save it as dicom file

Can you please help?

image

9

Hello,

I see the below error message “No patient found”. How can I fix this? Can you guide us? Is my SITK error issue due to DICOM file conversion?

image
image.png696×495 14.7 KB

10

I think you need to manually create a patient, and maybe a study too.

11

Hello,

This is a .nii file. So how do I create all details manually to .nii file? I mean if it’s dicom file, I can add missing tag information using Pydicom. but windering how can I do this for .nii

12

More information can be found in Data module’s documentation.

13

If you still have Slicer-related questions, Slicer forum is the right place for them.