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help > MP-RAGE structural scan (.nii) all chunky
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Jul 11, 2017 01:07 PM | James Bjork - Virginia Commonwealth University
MP-RAGE structural scan (.nii) all chunky
Hello,
I am giving the CONN toolbox a go, based on the informational youtubes (thanks!).
However, when I started a new project, and went to specify the structural MP-RAGE scan of a single subject (in .nii format initially reconstructed by the scanner), the image in the viewer is all chunky and pixelated at what looks to be 2-3mm voxel resolution. When I go to the "structural tools" to have a look, all I see is a blue screen/field at left of the image viewer, even though slicewise parameters are checked by default. Is there some reason CONN can't read this NIFTI file? I'll upload and attach a screenshot, but can your platform accommodate transmission of the MP-RAGE file itself?
Jim Bjork
(EDIT- I note that the file looks fine and crisp when I view it in AFNI)
I am giving the CONN toolbox a go, based on the informational youtubes (thanks!).
However, when I started a new project, and went to specify the structural MP-RAGE scan of a single subject (in .nii format initially reconstructed by the scanner), the image in the viewer is all chunky and pixelated at what looks to be 2-3mm voxel resolution. When I go to the "structural tools" to have a look, all I see is a blue screen/field at left of the image viewer, even though slicewise parameters are checked by default. Is there some reason CONN can't read this NIFTI file? I'll upload and attach a screenshot, but can your platform accommodate transmission of the MP-RAGE file itself?
Jim Bjork
(EDIT- I note that the file looks fine and crisp when I view it in AFNI)
Jul 20, 2017 02:07 AM | Alfonso Nieto-Castanon - Boston University
RE: MP-RAGE structural scan (.nii) all chunky
Hi James,
My guess is that this is perfectly fine, the reason why in the 'slice display' window you are not seeing anything may simply be because the voxel-to-world mapping in your mprage might be indicating that the brain coordinates are somewhat off the standard MNI bounding box. Simply unchecking the 'multi-slice display' checkbox in the GUI should allow you to see your anatomical file correctly. Please let me know otherwise
Hope this helps
Alfonso
Originally posted by James Bjork:
My guess is that this is perfectly fine, the reason why in the 'slice display' window you are not seeing anything may simply be because the voxel-to-world mapping in your mprage might be indicating that the brain coordinates are somewhat off the standard MNI bounding box. Simply unchecking the 'multi-slice display' checkbox in the GUI should allow you to see your anatomical file correctly. Please let me know otherwise
Hope this helps
Alfonso
Originally posted by James Bjork:
Hello,
I am giving the CONN toolbox a go, based on the informational youtubes (thanks!).
However, when I started a new project, and went to specify the structural MP-RAGE scan of a single subject (in .nii format initially reconstructed by the scanner), the image in the viewer is all chunky and pixelated at what looks to be 2-3mm voxel resolution. When I go to the "structural tools" to have a look, all I see is a blue screen/field at left of the image viewer, even though slicewise parameters are checked by default. Is there some reason CONN can't read this NIFTI file? I'll upload and attach a screenshot, but can your platform accommodate transmission of the MP-RAGE file itself?
Jim Bjork
(EDIT- I note that the file looks fine and crisp when I view it in AFNI)
I am giving the CONN toolbox a go, based on the informational youtubes (thanks!).
However, when I started a new project, and went to specify the structural MP-RAGE scan of a single subject (in .nii format initially reconstructed by the scanner), the image in the viewer is all chunky and pixelated at what looks to be 2-3mm voxel resolution. When I go to the "structural tools" to have a look, all I see is a blue screen/field at left of the image viewer, even though slicewise parameters are checked by default. Is there some reason CONN can't read this NIFTI file? I'll upload and attach a screenshot, but can your platform accommodate transmission of the MP-RAGE file itself?
Jim Bjork
(EDIT- I note that the file looks fine and crisp when I view it in AFNI)
Apr 18, 2019 05:04 PM | James Bjork - Virginia Commonwealth University
RE: MP-RAGE structural scan (.nii) all chunky
Hello Alfonso,
After a long hiatus, I now have some more bandwidth to explore CONN.
Same problem as before. I am amid the steps in your didactic YouTube series leading up to groupICA, and structural MRI is still chunky, even after toggling off multi-slice. Since the chunky structurals still look decently aligned with MNI boundaries, I'm forging ahead, but this is a bit disconcerting. I have uploaded a screenshot.
Jim
After a long hiatus, I now have some more bandwidth to explore CONN.
Same problem as before. I am amid the steps in your didactic YouTube series leading up to groupICA, and structural MRI is still chunky, even after toggling off multi-slice. Since the chunky structurals still look decently aligned with MNI boundaries, I'm forging ahead, but this is a bit disconcerting. I have uploaded a screenshot.
Jim