questions > Bvec Bval extraction in old MRI such as Siemens syngo MR 2004A
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May 24, 2018 02:05 PM | atouboul - Inria
Bvec Bval extraction in old MRI such as Siemens syngo MR 2004A
Dear Chris Rorden,
First I would like to thank you for your tool dcm2nii which is much appreciated by my team.
Secondly I have a small question on how do you extract Bvec Bval in diffusion images on an old MRI such as Siemens syngo MR. The issue we have is that we anonymize most of the private dicom tags prior we do the nifti conversion.
Using dcm2nii :
When I anonymize all private dicom tags, bvec/bval are not generated
When I anonymize the following all private tags except the list below, bvec/bval are not generated
Could you please let know which fields you are looking at in order to generate the bvec/bval ?
Thanks and best regards,
Arnaud
First I would like to thank you for your tool dcm2nii which is much appreciated by my team.
Secondly I have a small question on how do you extract Bvec Bval in diffusion images on an old MRI such as Siemens syngo MR. The issue we have is that we anonymize most of the private dicom tags prior we do the nifti conversion.
Using dcm2nii :
When I anonymize all private dicom tags, bvec/bval are not generated
When I anonymize the following all private tags except the list below, bvec/bval are not generated
- 0019; 100A; Number Of Images In Mosaic
- 0019; 100B; Slice Measurement Duration
- 0019; 100C; B_value
- 0019; 100D; Diffusion Directionality
- 0019; 100E; Diffusion Gradient Direction
- 0019; 100F; Gradient Mode
- 0019; 1027; B_matrix
- 0019; 1028; Bandwidth Per Pixel Phase Encode
Could you please let know which fields you are looking at in order to generate the bvec/bval ?
Thanks and best regards,
Arnaud
May 24, 2018 03:05 PM | Chris Rorden
RE: Bvec Bval extraction in old MRI such as Siemens syngo MR 2004A
Hello
In general, I would heed the warning generated by dcm2nii and upgrade to dcm2niix. However, in your case with such old data the older software may do a better job. Your data is from a Siemens system circa 2004, and pre-dates my archival sets
. Therefore, it is hard to provide advice, though your removal of private tags seems very extreme and goes far beyond normal anonymization. Perhaps you want to convert the raw data to NIfTI directly and skip the anonymization stage - it is much easier to create anonymized NIfTI images. My memory is hazy for such old images, in general the Siemens CSA headers are key to determine diffusion parameters (0029,1010 and 0029,1020). Please be careful to validate any bval and bvec files you get. Good luck!
In general, I would heed the warning generated by dcm2nii and upgrade to dcm2niix. However, in your case with such old data the older software may do a better job. Your data is from a Siemens system circa 2004, and pre-dates my archival sets
. Therefore, it is hard to provide advice, though your removal of private tags seems very extreme and goes far beyond normal anonymization. Perhaps you want to convert the raw data to NIfTI directly and skip the anonymization stage - it is much easier to create anonymized NIfTI images. My memory is hazy for such old images, in general the Siemens CSA headers are key to determine diffusion parameters (0029,1010 and 0029,1020). Please be careful to validate any bval and bvec files you get. Good luck!
May 25, 2018 07:05 AM | atouboul - Inria
RE: Bvec Bval extraction in old MRI such as Siemens syngo MR 2004A
Thank you very much Chris for the fast response.
It is working like a charm now.
It is working like a charm now.