Import data automatically to a volume node from a folder using command line

Tokai · March 19, 2020, 8:41pm

Operating system: win10
Slicer version: 4.10.2
Expected behavior:
Actual behavior:
Hi,
I have two folders containing .IMA files. I want to load them automatically into slicer using the folder paths and then perform registration between them.
So, I need to do first
# Load Volume
[ success,movingVolumeNode ] = slicer.util.loadVolume(Movinfilename,returnNode=True)
[ success, fixedVolumeNode] = slicer.util.loadVolume(Fixedfilename,returnNode=True)
And then
logic = SomeRegistrationLogic()
…
logic.registerVolumes(fixedVolumeNode, movingVolumeNode, outputVolumeNode)

But slicer.util.loadVolume takes a file not a directory. So my question is how can I import each of these directories using a python script and get them as volume node ?

pieper · March 19, 2020, 9:04pm

Hi -

By .IMA files I guess you mean dicom? You can try some of the methods in DICOMUtils. Also here’s a script that takes a directory of dicoms on the command line and makes volumes out of them. I haven’t tried this in a while and it may need some tweaking for the current Slicer.

github.com

QIICR/dcmheat/blob/master/docker/SlicerConvert.py

import os
import sys

def setDICOMReaderApproach(approach):
    import DICOMScalarVolumePlugin
    approaches = DICOMScalarVolumePlugin.DICOMScalarVolumePluginClass.readerApproaches()
    if approach not in approaches:
        raise ValueError("Unknown dicom approach: %s\nValid options are: %s" % (approach, approaches))
    approachIndex = approaches.index(approach)
    settings = qt.QSettings()
    settings.setValue('DICOM/ScalarVolume/ReaderApproach', approachIndex)


import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--dcmtk", help="use dcmtk to parse dicom (exclusive with --gdcm)", action="store_true")
parser.add_argument("--gdcm", help="use dcmtk to parse dicom (exclusive with --dcmtk)", action="store_true")
parser.add_argument("--no-quit", help="For debugging, don't exit Slicer after converting", action="store_true")
parser.add_argument("--input", help="Input DICOM directory")
parser.add_argument("--output", help="Output directory")

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Tokai · March 19, 2020, 9:53pm

Hi @pieper
The “db” error is fixed.
It would be db =slicer.app.dicomDatabase().
However it runs successfully and execute
"No scalar volumes parsed from the input DICOM dataset! Aborting."
Meaning no nodes!! Do you have any idea?
However it shows that it is imported in the slicer. But needs to be loaded in the GUI.

Tokai · March 19, 2020, 10:46pm

@pieper
I got another example from here.
dicomDataDir = “c:/my/folder/with/dicom-files” # input folder with DICOM files
loadedNodeIDs = [] # this list will contain the list of all loaded node IDs
from DICOMLib import DICOMUtils
with DICOMUtils.TemporaryDICOMDatabase() as db:
DICOMUtils.importDicom(dicomDataDir, db)
patientUIDs = db.patients()
for patientUID in patientUIDs:
loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))
But before I can check for volume node, it throws error:
loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))
TypeError: ‘bool’ object is not iterable

lassoan · March 19, 2020, 11:12pm

We recently reworked the DICOM browser. You need to use latest Slicer Preview Release for this last example (few days old release should be still OK, several weeks old may work differently).

Tokai · March 19, 2020, 11:20pm

Hi @lassoan,
Do you have any suggestion to fix this code (slicer 4.10.2) or another working example to load dicoms from folder and access as volume node using python scripting ?

lassoan · March 19, 2020, 11:55pm

Slicer-4.10 will soon be retired and Slicer-4.11 will be promoted to be the new stable release, so I would recommend to use most recent Slicer-4.11 version.

Tokai · March 20, 2020, 9:29am

@lassoan @pieper
So I found a simpler way. Simple providing the a single file of the folder in below method do the task. It loads all the files automatically.
slicer.util.loadVolume(‘single_file_of_folder’) .

Can you please tell me How can I set this loaded volume node as the fixed or moved volume from command line to perform landmark registration? I do not want use the gui.
Thanks

pieper · March 24, 2020, 7:56pm

Probably easiest to look at the self test code for ideas:

github.com

Slicer/LandmarkRegistration/blob/master/LandmarkRegistration.py#L984-L1013


      
              interator.SetControlKey(1)
            interator.SetEventPosition(*start)
            for step in range(steps):
              frac = float(step+1)/steps
              x = int(start[0] + frac*(end[0]-start[0]))
              y = int(start[1] + frac*(end[1]-start[1]))
              interator.SetEventPosition(x,y)
              style.OnMouseMove()
            interator.SetShiftKey(0)
            interator.SetControlKey(0)
          
          def setUp(self):
            """ Do whatever is needed to reset the state - typically a scene clear will be enough.
            """
            slicer.mrmlScene.Clear(0)
          
          def runTest(self,scenario=None):
            """Run as few or as many tests as needed here.
            """
            self.setUp()

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Tokai · March 24, 2020, 8:00pm

Hi @pieper,
I followed the exact example and it got solved
However, It is important that in my case I had to update the transform node from python script.

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Import data automatically to a volume node from a folder using command line

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