Operating system: win 10x 64
Slicer version:5.6.2
Expected behavior:
Actual behavior: showing errors which when i use the supplied software…given to me intelerad.inteleviewer all files display as intended. The version is from 2016 and 4-8-1-p125 if that iis of help …so i can see the spinal collum. I have tried every turtorial a possibly can/able to do.Then found the pull out collum to show errors to me. I dont know how to grab attention for help on here so i tried the Horder center which is where MRI came from. Sadly the person whom took care for years of me has retired and was going to assist me. I am designing an implant for a certain condition and aim to implant in myself… Hence a previous post to convert so i can implement into solidworks.I need a ref model to design around for a base line model/protoype
Loading an image acquired by a clinical scanner should be no problem. Please provide more information or an anonymized data set.
Hi Thanks for replying. The dicom files i have are on cd from the MRI which has the inteleviewer software to see all on the disc/from disc. The files are in a folder PA under the DICOM icon.When i try and import via add data" i have a desk top save location created" , there seems to be errors showing…via the x on lower right. I am trying to create the stl so i can model in solidworks. I have base designs on paper and need to make it a model. I have engineering skills to design and the know how in order to make it, but not in this medical field. I am looking at the Lumber facet area of the scan if that helps.The errors are python and citical error …i will ask DOES 3d slider have to be installed on the same drive as the O/S? just a thought… Thank you for any help in advance…
The error messages are not visible in your screenshots. Please select all the messages, copy them, and then paste them here. Remove any patient information that may appear in the messages.
Hi, when i went to copy them it showed this below which i was then able to copy paste. Is this correct?
Switch to module: “DICOM”
TagCacheDatabase adding table
“DICOM indexer has successfully processed 0 files [0.00s]”
“DICOM indexer has updated display fields for 0 files [0.00s]”
Imported a DICOM directory, checking for extensions
Could not load “F:/DICOM/PA000001/ST000001/SE000001/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000001/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000002/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000002/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000003/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000003/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000004/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000004/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000005/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000005/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000006/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000006/SeriesHeader.zip
“DICOM indexer has successfully inserted 124 files [20.23s]”
“DICOM indexer has successfully processed 130 files [58.22s]”
“DICOM indexer has updated display fields for 124 files [0.09s]”
Imported a DICOM directory, checking for extensions
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Geometric issues were found with 1 of the series. Please use caution.
Warning in DICOM plugin Scalar Volume when examining loadable 1: L SPINE: Reference image in series does not contain geometry information. Please use caution.
Warnings detected during load. Examine data in Advanced mode for details. Load anyway?
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=128.0, width=256.0) has been applied to volume 1: L SPINE
No geometry information available for DICOM data, skipping corner calculations
Could not load “F:/DICOM/PA000001/ST000001/SE000001/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000001/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000002/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000002/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000003/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000003/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000004/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000004/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000005/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000005/SeriesHeader.zip
Could not load “F:/DICOM/PA000001/ST000001/SE000006/SeriesHeader.zip”
DCMTK says: I/O suspension or premature end of stream
Could not read DICOM file:F:/DICOM/PA000001/ST000001/SE000006/SeriesHeader.zip
“DICOM indexer has successfully inserted 124 files [0.34s]”
“DICOM indexer has successfully processed 130 files [5.31s]”
“DICOM indexer has updated display fields for 0 files [0.09s]”
Imported a DICOM directory, checking for extensions
Warning in DICOM plugin Scalar Volume when examining loadable 501: TRA T1 TSE: Image slices are not equally spaced (0 spacing was expected, 4.39999 spacing was found between files C:/Users/xxxxxxxxxx/Desktop/back/ctkDICOM-Database/dicom/2f1a7fa4/06a3b628/ede4edc57d222979c0e6a33445b91497.dcm and C:/Users/xxxxxxxxx/Desktop/back/ctkDICOM-Database/dicom/2f1a7fa4/06a3b628/5b54119c34e5bdf5f8ba273962d4449b.dcm). Slicer will apply a transform to this series trying to regularize the volume. Please use caution.
It seems that you got 2D pictures, without any information about where they are in 3D space. The presence of those zip files are unusual, too. Are these the original files ghat tou received from the hospital or they are processed with some software?
Could you copy the logs you get if you enable detailed logging in application settings / DICOM section?
Hi,
The files were placed on a CD using intelerad viewer software which i put in a prev post you possible read. The files on the disc are purley in a dicom file and are direct off the disc from the center i was at with intelerad to look at the files.scans. I have copied the disc but the files MB etc is all in order. These are from 2016-2017 if thats of help and a paid for them for this purpose back then. 3D i will check today in inteleviewer as i have a navigator so it will be easy to see and get back to you . Unless thats has restricted the options but it does not explain slicer.data itself. I am with you on that note.
With ref to logging details i will check on that also as this is new ground and i have only installed slicer the past week…5.7 was not working so i went to 5.6 now i know it was poss my data. That may be an issue as its past 7 years almost. I 
will revert back later today
Hi,
I have an update. Thanks on the 2D part as tbh i did wonder when i could not use my navigator in inteleviewer.
1st it may appear i only have 2d files. Why i am not sure maybe due to getting printed into photos. I have spoken to the scan people and i await. My file may be too old ie 7 years which will be a blow like no other if thats the case.
Plan B is i am hoping if this is the case, help here can assist if possible to exract or find a way with slicer can regerate into 3d or into anything that allows me to break it down or use the model as is . I can design the implant around that as long as solidworks can import it.
Plan C is hunt for a surgeon and join forces.
i will keep you updated…
It may be possible to force reconstructing a volume by enabling “Advanced” option in the DICOM browser and trying all offered loadables (check all the checkboxes in the advanced section) and then manually set spacing in Volumes module (Volume Information section).
Hi,
I will look into that and see what i can learn over the next few days thankyou. In the mean time i have been in touch and found out my file is pos still there, and i hope to get a copy in 3D…in the mean time i will try the process you mentioned, even if i fail badly atleast it gives a learning curve. Once i have the correct files to start with then i have a fighting chance of success. I will keep you informed as its good for others whom may have simular issues. 3d SLICERS ability for 3D, am i correct if i set and allow CUDA cores for 3D slicer it will utilise them?..Windows has not reign on my GPU hence the ?..Thankyou
If you have a good GPU then it makes certain operations faster. In general,
you should be fine with or without a GPU.
Hi,
Currently…Still awaiting the file. In the mean time i have had a look into what you said. It took a little bit to try and understand what you were educating me try. In short the GUI did leave many unchecked. So the result is still many errors python etcITK and so fourth. Under loaded data there are many in the list and tbh much i dont have a clue about. Barr 1 file which is the linear view/BIV depending on your perspective. The rest are small slices…no pun intended which dont allow me to see much.Nore do i know what they are which indicates maybe i should wait and have the proper files then to learn should less harder. Hoping the new files have no errors then atleast its a good base to start from Vs corrupt files and little knowhow. I will be in touch but wanted to say i have tried but im just getting confused…
Hi, I have an update. I recieved the files, incl a viewer…weasis? Anyhow this opens the files in 2D, i am not 100% my files are in fact 3D but yet to find out… Chances are its right in front of me.
These files imported ok, i followed as much as possible to what you mentioned…check box,s checked and the box noting issues and to try and repair. Which i assume is what utilities ref too? and i hope i did correct…if not then thats for later.
I saved the files to a seperate location vs the imported files i have. Thats also was a note to try on the slicer help page i read…
Currently i only see the blue box…image area and 1 part of the spine and 2 thin slices… However i have many files saved with CTK files x 2 and image orientation seq.mrb with a slicer logo/thumbnail and nrrd files. There is also 1 file which coccyx…so is there a file which ref the whole spine section scanned, or will it need to be extracted/generated.
Do you have a guide for dummies, also ref to certain things of the main GUI icons etc as i have no indication as to where they all are are and some tutorials ref say utilities. As i read i may need a patcher? this is under Tutorials
https://slicer.readthedocs.io/en/latest/user_guide/modules/dicompatcher.html
As long as i can get a 1.1 ratio into solidworks via any means stl stp etc… the rest is more in my comfort zone.
Hi,
I have heard back with ref to the files. They are in 2D as the 3D it seems are only for certain requirements. I estimate this is down to the treatment a patient would be getting. Disc replacement or some thing of that nature operation wise.
So this beggs the question of is there a way a novice can convert or extract it with out to much in the way of issues please that will help me. I know this will not be 100% accurate to scale may be 1.1 ratio is to much to ask, but a close 1 will be a useable model in solidworks.
The only other option is another SCAN in 3D which is not possible currently. Its a bit of a Blow but this does answer the questions for some i hope that MRI are only in 3D if thats required/requested, and as to the type of the health care a individual has.I assume a 3D in full would take longer and cost alot more.
HI all, Update i am hoping to get things moving early next year is there a book or a tutorial in the newest versin i can do from scratch to learn how to convert extract a flat 2 image into 3D with ending up the spine looking like a slinky ranover. The issue lies in the versions i am trying to learn and educate from are are not what i have. And much i find to guide does not relate to my issues soley…I am not scared to learn but i wish to learn what is correct.
Thank you