questions > Problems converting DICOM in NiFTI with data from a 3T GE 750
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Apr 9, 2023 12:04 PM | Antonio Innocenzi
Problems converting DICOM in NiFTI with data from a 3T GE 750
Hi everybody, I'm an italian radiology resident. I'm trying
converting a DWI DICOM file folder in NiFTI, in order to obtain a
.mat file, usable on Explore DTI or FSL.
I've tried multiple tools as explore DTI plugin or MrICRO. Using the last one i obtain these problems:
"DICOM images may be missing, expected 50 spatial locations per volume, but found 25.
Warning: Unable to determine GE Slice timing, no Protocol Data Block GE (0025,101B): C:\Users\HP\Desktop\Sequenze prova\DWI 2 prova - Copia\dwi\UD02XKTM\CV0UEYHL\I1000000
Note: B0 not the first volume in the series (FSL eddy reference volume is 1)
Warning: Some images had bval>0 but bvec=0 (either Trace or b=0, see issue 245)
Note: this appears to be a b=0+trace DWI; ADC/trace removal has been disabled.
Maximizing 16-bit range: raw 0..5025 is6".
I can use a 3T MRI GE750. Can someone help me understanding the reasons of these problems and, eventually, possible solutions?
Best regards,
Antonio
I've tried multiple tools as explore DTI plugin or MrICRO. Using the last one i obtain these problems:
"DICOM images may be missing, expected 50 spatial locations per volume, but found 25.
Warning: Unable to determine GE Slice timing, no Protocol Data Block GE (0025,101B): C:\Users\HP\Desktop\Sequenze prova\DWI 2 prova - Copia\dwi\UD02XKTM\CV0UEYHL\I1000000
Note: B0 not the first volume in the series (FSL eddy reference volume is 1)
Warning: Some images had bval>0 but bvec=0 (either Trace or b=0, see issue 245)
Note: this appears to be a b=0+trace DWI; ADC/trace removal has been disabled.
Maximizing 16-bit range: raw 0..5025 is6".
I can use a 3T MRI GE750. Can someone help me understanding the reasons of these problems and, eventually, possible solutions?
Best regards,
Antonio
Apr 9, 2023 01:04 PM | Chris Rorden
RE: Problems converting DICOM in NiFTI with data from a 3T GE 750
Your questions is underspecified to provide a diagnosis. Details
like the version of dcm2niix you are using would help, as well as
the full details to replicate. I would suggest you file an `issue`
for dcm2niix:
https://github.com/rordenlab/dcm2niix
the template will guide you through the details that help providing feedback.
My first guess is that an anonymization tool has stripped out the DICOM tags that are vital for determining sequence details:
https://github.com/rordenlab/dcm2niix/tree/master/GE
I suggest you check the provenance of your images. Specifically, a direct export from the scanner should include the private tag 0025,101B.
https://github.com/rordenlab/dcm2niix
the template will guide you through the details that help providing feedback.
My first guess is that an anonymization tool has stripped out the DICOM tags that are vital for determining sequence details:
https://github.com/rordenlab/dcm2niix/tree/master/GE
I suggest you check the provenance of your images. Specifically, a direct export from the scanner should include the private tag 0025,101B.