"How to" for a really newbie having a MRI CDRom?

Support
1

Operating system: Win10
Slicer version: 4.10.2
Expected behavior: Obtaining 3D model of my head
Actual behavior: Seeing images but not sure the good way

Hi, I’m really new to 3D Slicer and all of those MRI stuff.
I’m french, so you can contact me in this language if you want.

I’ve got a recent MRI of a head on a CD-ROM.
The directory structure of the CD-ROM is shown below :
image
As you can see, there is no file extension. But the files are DICOM files from an Optima MR360 (as seen in a hexadecimal version of one of a DICOM files).

I’m trying to load those files in Slicer 3D.

First question : Can I load all the SE1, SE2, SE3, SE4, … SE8 folders, or should I load only one ?

When loading just one file by dragging and dropping the first file, it’s ok :

image
image897×524 62 KB

I choose the “Show options” and deselect “Single file”, then I press OK.

image
image743×205 7.88 KB

I choose the “Volumes” module, and display “Volume information”.

image
image607×560 28.1 KB

Second question : Do I need to chance something on this “Volumes” module ?

I try next to use the “Vector to scalar” module, but I really don’t know if it’s necessary, or what to do (the input vector volume dropdown list is empty).
image

If I choose the “Volume rendering” module, and playing with “Preset” dropdown list, I obtain (after clicking on the closed eye next to “Volume :” label) a king of 3D, but that’s not a head…

image
image1359×338 118 KB

Question 3 : Can you help me to have a good result with the CDRom datas ?

Cordially

Janolap1

2

What you have is DICOM data, so you will need to import it (the folder PA1) to the DICOM database using the DICOM browser and load from there.
https://www.slicer.org/wiki/Documentation/Nightly/Modules/DICOM#Data_import_and_loading

3

Thank you @cpinter !
I think there is a issue with the DICOM Browser.
I don’t know where is the option to “Show DICOM browser”.

And when I read the error windows, there is a critical error when launching the DICOM module :

Traceback (most recent call last):
File "C:/Program Files/Slicer 4.10.2/bin/../lib/Slicer-4.10/qt-scripted-modules/DICOM.py", line 360, in setup
self.detailsPopup = self.getSavedDICOMDetailsWidgetType()()
File "C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 1015, in __init__
super(DICOMDetailsWindow, self).__init__(dicomBrowser, parent)
File "C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 984, in __init__
DICOMDetailsBase.__init__(self, dicomBrowser)
File "C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 93, in __init__
self.promptForDatabaseDirectory()
File "C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 540, in promptForDatabaseDirectory
os.makedirs(databaseDirectory)
File "C:/Program Files/Slicer 4.10.2/bin/../lib/Python/Lib\os.py", line 157, in makedirs
mkdir(name, mode)
WindowsError: [Error 2] Le fichier sp�cifi� est introuvable: u'C:/Users/jean/Documents\\SlicerDICOMDatabase'
Traceback (most recent call last):
File "C:/Program Files/Slicer 4.10.2/bin/../lib/Slicer-4.10/qt-scripted-modules/DICOM.py", line 301, in enter
self.onOpenDetailsPopup()
File "C:/Program Files/Slicer 4.10.2/bin/../lib/Slicer-4.10/qt-scripted-modules/DICOM.py", line 401, in onOpenDetailsPopup
if not isinstance(self.detailsPopup, self.getSavedDICOMDetailsWidgetType()):
AttributeError: DICOMWidget instance has no attribute 'detailsPopup'
Traceback (most recent call last):
File "C:/Program Files/Slicer 4.10.2/bin/../lib/Slicer-4.10/qt-scripted-modules/DICOM.py", line 234, in dropEvent
dicomWidget.detailsPopup.dicomBrowser.importDirectories(self.directoriesToAdd)
AttributeError: DICOMWidget instance has no attribute 'detailsPopup'

I think I have a bug ? isn’t it ?

Can you help me once again ?

Thank you

janolap1

4

I would recommend to try with latest Slicer Preview Release, as it contains fixes for many common issues with the DICOM browser.

1 Like
5

Thank you !
No problem with the preview release.

1 Like