Closed MatthewKoffPhD closed 4 years ago
Hi Matt,
Since you have C:
, I guess you are using Windows. In your input file, change all the /
to \
. Your input file should become like this:
C:\temp\demo_knee\inputs\original
01\DESS\01
right
01\DESS\02
right
01\cubeQuant\01
right
01\cubeQuant\02
right
01\cubeQuant\03
right
01\cubeQuant\04
right
Please, let me know if it works. Thanks, Serena
D'oh. That was it.
Also, in an effort to move the process along, I skipped the field_correction step, but it appears that the following rescale_to_range step needs input filenames names like: '[name]_temp.mha'.
Can I manually rename the files: 01_DESS_01_orig.mha --> 01_DESS_01_temp.mha and get the rescaling and subsequent subroutines to work?
Thanks!
On Fri, Feb 14, 2020 at 5:05 AM Serena Bonaretti notifications@github.com wrote:
Hi Matt, Since you have C:, I guess you are using Windows. In your input file, change all the / to . Your input file should become like this:
C:\temp\demo_knee\inputs\original 01\DESS\01 right 01\DESS\02 right 01\cubeQuant\01 right 01\cubeQuant\02 right 01\cubeQuant\03 right 01\cubeQuant\04 right
Please, let me know if it works. Thanks, Serena
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yes, that should work!
Hi,
I'm going through the tutorial, starting with preprocessing, but it appears that subdirectories are not being created in Step 0: read the dicom images
My mage_list_preprocessing.txt file looks like this: C:/temp/demo_knee/inputs/original 01/DESS/01 right 01/DESS/02 right 01/cubeQuant/01 right 01/cubeQuant/02 right 01/cubeQuant/03 right 01/cubeQuant/04 right
Reading the image data using: image_data = io.load_image_data_preprocessing(input_file_name) is ok and works
However, the next step: prep.read_dicom_stack(image_data, n_of_cores), gives me the error: RuntimeError: Exception thrown in SimpleITK WriteImage: D:\a\1\sitk-build\ITK\Modules\IO\Meta\src\itkMetaImageIO.cxx:1129: itk::ERROR: MetaImageIO(000001BD1FFB0080): File cannot be written: C:/temp/demo_knee/inputs\preprocessed\01/DESS/01_temp.mha Reason: No such file or directory
When I manually create /demo_knee/inputs/preprocessed/01/DESS, then it puts in the 2 files: 01_temp.mha and 02_temp.mha.
Similarly, I need to manually create the /demo_knee/inputs/preprocessed/01/cubeQuant, where it places 01_temp.mha, 02_temp.mha, 03_temp.mha, 04_temp.mha.
Should all of these subdirectories be created automatically?
Looking forward to using the software!