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spinal-cord-7t / coil-qc-code

7T Spinal Cord Coil QC Analysis Code
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Phantom sub-MSSM_acq-coilQaTra_GFactor file appears to be corrupt #61

Open evaalonsoortiz opened 2 months ago

evaalonsoortiz commented 2 months ago

When viewing the file in python, it appears blank:

image

If I try to open the nifti with fsleyes I get the following error:

Screen Shot 2024-05-01 at 12 46 12 PM

@Kyota-exe Have you been able to open this file? Are you certain the correct file was converted?

evaalonsoortiz commented 2 months ago

Update: it appears that the dicom to nifti conversion is not working for these scans for the following reason:

/Volumes/MRIcroGL/MRIcroGL.app/Contents/Resources/dcm2niix -f "%f_%p_%t_%s" -p y -z y "/Users/evaalonsoortiz/Desktop/scans/33_GFactor/DICOM/spinoza_v6_phantom.MR.RESEARCH_GCO-20-8888D-A_Seifert.33.1.20230622.120932.c36bkw.dcm"
Compression will be faster with 'pigz' installed http://macappstore.org/pigz/
Chris Rorden's dcm2niiX version v1.0.20220720  Clang12.0.5 ARM (64-bit MacOS)
Found 312 DICOM file(s)
Warning: Siemens MoCo? Bogus slice timing (range -1..-1, TR=0 seconds)
Warning: Unable to determine slice direction: please check whether slices are flipped
Convert 312 DICOM as /Users/evaalonsoortiz/Desktop/scans/33_GFactor/DICOM/DICOM_CoilQA_sag_HF_FOV192_1p5x1p5x2p0_20230622120933_33b (256x256x13x24)
Conversion required 3.493886 seconds (1.143389 for core code).

I can visualize the dicoms with Horos, but the conversion is not possible using dcm2niix due to some slice timing header issues ...

Screen Shot 2024-05-02 at 12 28 48 PM

I will remove these scans from the analysis for now. If anyone can test alternative dicom to nifti converters (or let me know if their existence?) that would be appreciated.