open-discussion > Dicom bold images misalignment?
Showing 1-4 of 4 posts
Apr 21, 2020 01:04 PM | Yun Tian - Southwest University
Dicom bold images misalignment?
There are dozens of subjects (focused on the early stage of the
project) that appears "misaligned" in the raw bold images and dti
images, but there is no problem in T1-weighted images obtained at
the same time. The scanner is Siemens 3-T prism.
I attach a bold image screenshot. I don't know how to describe this problem, 'misalignment'? The brain image that should be at the top seems to appear at the bottom.
Is there any body knows how to fix this issue? Extremely grateful!
I attach a bold image screenshot. I don't know how to describe this problem, 'misalignment'? The brain image that should be at the top seems to appear at the bottom.
Is there any body knows how to fix this issue? Extremely grateful!
Apr 21, 2020 02:04 PM | Alex Dresner
_Dicom_bold_imag?==?windows-1258?Q?es_misalignment=EF=BC=9F?=
This is image offset and phase wrap. The images were acquired
offcenter and the representation of the anatomy that would have
been outside of the field of view (FOV) appears on the other side
of the image. Standard image registration tools are not designed to
correct for this, but it shouldn�t be hard to build something that
shifts pixels in a circular fashion to correct for it. (Then you
can use standard tools for the actual registration.)
Apr 21, 2020 02:04 PM | Mehran Azimbagirad
RE: Dicom bold images misalignment?
Try to open it with other tools like Slicer or ITKSnap. If the
problem is still there, you should find out how many voxels are
misaligned. And for all images is the same size or not. If so, you
can reconstruct the image easily by python and sitk module.
Apr 21, 2020 02:04 PM | Paul Camacho - University of Illinois at Urbana-Champaign
RE: Dicom bold images misalignment?
It looks like the origin of the images
has been translated some 20 to 30% in the anterior
direction. I'm sure someone has a better fix for this issue,
but these are the troubleshooting steps I would look at
first.
Does this translation persist when you convert the raw DICOMs to NIFTI files? If so, then you might want to check the DICOM headers (I use AFNI's dicom_hdr command line tool). Are the origin points in the DICOM headers for your BOLD and DTI images consistent with those of your T1w images? If they do not appear to be consistent, you can try adjusting the relevant DICOM tags (https://www.dicomlibrary.com/dicom/dicom...) by whatever the common difference is or use the SPM reorient GUI to manually set new origin points based on the anterior commissure and perform a translation.
Best of luck!
Originally posted by Yun Tian:
Does this translation persist when you convert the raw DICOMs to NIFTI files? If so, then you might want to check the DICOM headers (I use AFNI's dicom_hdr command line tool). Are the origin points in the DICOM headers for your BOLD and DTI images consistent with those of your T1w images? If they do not appear to be consistent, you can try adjusting the relevant DICOM tags (https://www.dicomlibrary.com/dicom/dicom...) by whatever the common difference is or use the SPM reorient GUI to manually set new origin points based on the anterior commissure and perform a translation.
Best of luck!
Originally posted by Yun Tian:
There are dozens of subjects (focused on the
early stage of the project) that appears "misaligned" in the raw
bold images and dti images, but there is no problem in T1-weighted
images obtained at the same time. The scanner is Siemens 3-T
prism.
I attach a bold image screenshot. I don't know how to describe this problem, 'misalignment'? The brain image that should be at the top seems to appear at the bottom.
Is there any body knows how to fix this issue? Extremely grateful!
I attach a bold image screenshot. I don't know how to describe this problem, 'misalignment'? The brain image that should be at the top seems to appear at the bottom.
Is there any body knows how to fix this issue? Extremely grateful!