animaDiffusionImagePreprocessing.py

[Lorenzomarta]

Hi everyone,
I am working with Anima to study the evolution of a glioblastoma. I am having difficulty in the per-processing phase to obtain the files necessary to associate the mesh with the diffusion values ​​obtained from magnetic resonance from a DTI files.
In particular, following the guide https://anima.readthedocs.io/en/latest/diffusion_scripts.html#diffusion-images-preprocessing-script
I get the following output from the files indicated as necessary in the line of code to be launched from the terminal:

'''
(base) MAC-2: Preprocessing lorenzomarta $ python3 animaDiffusionImagePreprocessing.py -b Diff.bval -D DTI_64_dir_B3000_501 / * -d 1 -t T1.nii.gz -i Diff.nii.gz
Traceback (most recent call last):
File "/Users/lorenzomarta/Desktop/Preprocessing/animaDiffusionImagePreprocessing.py", line 131, in
bval = image [0x5200, 0x9230] .value [0] [0x0018, 0x9117] .value [0] [0x0018, 0x9087] .value
File "/Users/lorenzomarta/Library/Python/3.9/lib/python/site-packages/pydicom/dataset.py", line 916, in getitem
elem = self._dict [tag]
KeyError: (5200, 9230)
'''

where DTI_64_dir_B3000_501 is my DICOM folder.

I do not understand the error. How can I proceed?

[rhedouin]

Hi Lorenzo, I think the way the script work, you're suppose to give all the dicom files instead all the dicom folder, i.e a list of all the dicom in your dicom folder (I know that it's not really practical). Tell me if you need anything else, Best, Renaud Le lun. 2 mai 2022 à 17:53, Lorenzomarta ***@***.***> a écrit :

…

Hi everyone, I am working with Anima to study the evolution of a glioblastoma. I am having difficulty in the per-processing phase to obtain the files necessary to associate the mesh with the diffusion values ​​obtained from magnetic resonance from a DTI files. In particular, following the guide https://anima.readthedocs.io/en/latest/diffusion_scripts.html#diffusion-images-preprocessing-script I get the following output from the files indicated as necessary in the line of code to be launched from the terminal: ''' (base) MAC-2: Preprocessing lorenzomarta $ python3 animaDiffusionImagePreprocessing.py -b Diff.bval -D DTI_64_dir_B3000_501 / * -d 1 -t T1.nii.gz -i Diff.nii.gz Traceback (most recent call last): File "/Users/lorenzomarta/Desktop/Preprocessing/animaDiffusionImagePreprocessing.py", line 131, in bval = image [0x5200, 0x9230] .value [0] [0x0018, 0x9117] .value [0] [0x0018, 0x9087] .value File "/Users/lorenzomarta/Library/Python/3.9/lib/python/site-packages/pydicom/dataset.py", line 916, in getitem elem = self._dict [tag] KeyError: (5200, 9230) ''' where DTI_64_dir_B3000_501 is my DICOM folder. I do not understand the error. How can I proceed? — Reply to this email directly, view it on GitHub <#87>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQLXM22XKAUM322KETEUIDVH73AXANCNFSM5U4L3QEA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Lorenzomarta]

How could I do that?

[rhedouin]

You can do something like this (following you example) myCommand="python3 animaDiffusionImagePreprocessing.py -b Diff.bval -d 1 -t T1.nii.gz -i Diff.nii.gz -D" for dicom in DTI_64_dir_B3000_501 / *; do myCommand="$myCommand $dicom" done That should give you a command that work that just can just lunch in a terminal something that look pretty scary like /home/rhedouin/Software/Anima-Scripts-Public/diffusion/animaDiffusionImagePreprocessing.py -b 13_BC_noddi.bval -t ../../../Structural/T13D/13_BC_T13D.nii.gz -i 13_BC_noddi.nii.gz -r 13_BC_noddi_reversed_b0.nii.gz -D 13_BC_noddi_dicom/1.4.9.12.34.1.8527.1007454200340373658590858113205624300406.dcm 13_BC_noddi_dicom/1.4.9.12.34.1.8527.1080927551794522828572421740250709057251.dcm 13_BC_noddi_dicom/1.4.9.12.34.1.8527.1128132512393588910212288014868857030725.dcm 13_BC_noddi_dicom/1.4.9.12.34.1.8527.1133722950676801911874724089147898492160.dcm 13_BC_noddi_dicom/1.4.9.12.34.1.8527.1165275000797006852681624288247869655076.dcm 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13_BC_noddi_dicom/1.4.9.12.34.1.8527.9247712850066646862283286242767814332425.dcm 13_BC_noddi_dicom/1.4.9.12.34.1.8527.9304183773505720487750769916882925194870.dcm Le mer. 4 mai 2022 à 17:50, Lorenzomarta ***@***.***> a écrit :

…

How could I do that? — Reply to this email directly, view it on GitHub <#87 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQLXM6SAGT5YWDUOS6NSLDVIKMDJANCNFSM5U4L3QEA> . You are receiving this because you commented.Message ID: ***@***.*** com>

[Lorenzomarta]

I have a doubt, should I write these commands directly from the terminal? or on a file and then launch it? Sorry but I'm not very experienced

[ocommowi]

Hi,

I will keep only this discussion active and may be close the others which are duplicates.

In fact the script does not convert dicom files to nifti (there are so many ways I prefer to let that to the user), so you cannot pass the dicom files directly to the script. You should convert first your dicom to nifti using eg dcm2niix or mrconvert that work usually well.

The -D option that was mentioned above has only been tested for siemens scanner and its goal is to correct the bvec files that is sometimes flipped along some axes for those scanners after dicom conversion.

Hope this helps