[color=#000000]Hi James,[/color]
[color=#000000]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[/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by James Bjork:[/i][quote]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)[/quote]
[color=#000000]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[/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by James Bjork:[/i][quote]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)[/quote]