Regularization issue

Support
1

HI Slice Community,

I have been struggling for certain amount of time regarding what I have understand to be regularization.

I have a MRI of different areas encapsulated in one acquisition.
I just would like to have “blank” slices in the coordinate where there is no acquisition. With regularization activated, there is no distorsion but Slicer make weird stuff between the areas.

I Watch the image information and there were issues with th order. For example n°5 slice beiing in fact n°4 when regarding the coordinate. I changed all names but didn’t make any difference. I guess slice already made the correction.

You will find informations below.

Thanks very much for your help

JR

image

M0001 ImagePositionPatient [3] -150.300, -100.000, 21.000
M0002 ImagePositionPatient [3] -150.300, -100.000, 18.500
0003- ImagePositionPatient [3] -150.300, -100.000, 16.000
M0004 ImagePositionPatient [3] -150.300, -100.000, 13.500
0005- ImagePositionPatient [3] -150.300, -100.000, 11.000
0006- ImagePositionPatient [3] -150.300, -100.000, 8.500
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0008- ImagePositionPatient [3] -150.300, -100.000, 3.500
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M0018 ImagePositionPatient [3] -150.300, -100.000, -21.500
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M0322 ImagePositionPatient [3] -150.300, -100.000, -857.500
M0323 ImagePositionPatient [3] -150.300, -100.000, -860.000
0324- ImagePositionPatient [3] -150.300, -100.000, -862.500
0325- ImagePositionPatient [3] -150.300, -100.000, -865.000
M0326 ImagePositionPatient [3] -150.300, -100.000, -867.500
M0327 ImagePositionPatient [3] -150.300, -100.000, -870.000
M0328 ImagePositionPatient [3] -150.300, -100.000, -872.500
M0329 ImagePositionPatient [3] -150.300, -100.000, -875.000
0330- ImagePositionPatient [3] -150.300, -100.000, -877.500
0331- ImagePositionPatient [3] -150.300, -100.000, -880.000
M0332 ImagePositionPatient [3] -150.300, -100.000, -882.500
0333- ImagePositionPatient [3] -150.300, -100.000, -885.000
0334- ImagePositionPatient [3] -150.300, -100.000, -887.500
0335- ImagePositionPatient [3] -150.300, -100.000, -890.000
M0336 ImagePositionPatient [3] -150.300, -100.000, -892.500
M0337 ImagePositionPatient [3] -150.300, -100.000, -895.000
M0338 ImagePositionPatient [3] -150.300, -100.000, -897.500
M0339 ImagePositionPatient [3] -150.300, -100.000, -900.000
M0340 ImagePositionPatient [3] -150.300, -100.000, -902.500
0341- ImagePositionPatient [3] -150.300, -100.000, -905.000
0342- ImagePositionPatient [3] -150.300, -100.000, -907.500
M0343 ImagePositionPatient [3] -150.300, -100.000, -910.000
M0344 ImagePositionPatient [3] -150.300, -100.000, -912.500
M0345 ImagePositionPatient [3] -150.300, -100.000, -915.000
M0346 ImagePositionPatient [3] -150.300, -100.000, -917.500
M0347 ImagePositionPatient [3] -150.300, -100.000, -920.000
M0348 ImagePositionPatient [3] -150.300, -100.000, -922.500
2

In DICOM data sets, file names are ignored. Image slices are placed in position and orientation prescribed by “image position patient” and “image orientation patient” fields embedded in the file.

If slices are not spaced equally then you have no other option than enabling regularization. If there are artifacts then most probably the frames contain inconsistent information (image content is not consistent with its position and orientation). You may inspect the files using DICOM browser / Metadata feature to identify offending frames, remove them, clear the database, and re-import the data set without the inconsistent frames.

3

Thanks very much. I’ll go through this process then.
appriciate your feedbacks, helps a lot.
JR

4

@lassoan, I tried to have a look but didn’t find anything satisfying. However I really don’t understand why Slicer is trying to reconstruct something beetween -91,5 / - 383,250 and -538.250 / -792.5 as there is no slices. may be I misunderstand what he is doing…
Finaly the “harden transform” and and the “segment editor” are impossible to use. Slicer freezes everytime I lunch theses module with this scene. Normaly it works perfectly.

Thanks again for your insights,
Sincerely,

JR

5

Hi Slice community,

If anyone has some advice or things I could try…
The fact is that we have an MRI with different slices height and gaps between each body part ie: Ankle with slices height 1 --> blank --> knee with slices height 2 --> blank --> hip with slices height 3. I tried to check if there were inconsistencies as @lassoan suggested but everything seems ok except that Slicer is trying to “make” slices in the gaps which causes problems I think. Is there a way in the regularization process to indicate not to “fill” the gaps?
Regards,

JR

6

Depending on how large the image is and how much memory you have, you may need to wait a very long time.

One image series is always loaded as one contiguous block of image. If you want to load them separately then they should have saved as separate image series. You might be able to load subvolumes by series time, if you enable menu: Edit / Application settings / DICOM / “Allow loading subseries by time” and enable Advanced mode in DICOM module. You may also split the volume manually by moving selected image slices into separate subfolders and loading them using “Add data” (instead of DICOM module), because “Add data” only looks into the current folder.