Hi,
I tried using dcm2niix_afni to convert my GE DTI blip up / blip down dicom data to NIFTI format. In doing so, I realized that the .bval files that were created did not seem accurate. Every shell had the maximum bval of 1100 except for the first one, which was zero. I think this may be due to a problem with the GE Dicom headers. I found that a previous user in my group extracted the information about bvalues using a cdiflist file. Seeing that AFNI has a function called `convert_cdiflist_to_grads.py` to extract the gradients from this cdiflist file, I ran this command:
convert_cdiflist_to_grads.py -cdiflist cdiflist45 -bval_max 1100 -prefix test
My file called cdiflist45 looks like this:
45
0.00 0.00 0.00
0.426 0.00 0.00
0.19 0.381 0.00
0.19 0.117 0.363
0.00 0.00 0.00
0.674 0.00 0.00
0.301 0.603 0.00
0.301 0.185 0.574
1.00 0.00 0.00
0.166 0.986 0.00
-0.110 0.664 0.740
0.901 -0.419 -0.110
-0.169-0.601 0.781
-0.815 -0.386 0.433
0.656 0.366 0.660
0.582 0.800 0.143
0.900 0.259 0.350
0.693 -0.698 0.178
0.357 -0.924 -0.140
0.543 -0.488 -0.683
-0.525 -0.396 0.753
-0.639 0.689 0.341
-0.330 -0.013 -0.944
0.00 0.00 0.00
0.191 -0.308 -0.224
0.19 -0.308 0.224
-0.191 -0.118 0.362
0.302 -0.487 -0.354
0.301 -0.488 0.355
-0.303 -0.187 0.573
-0.524 -0.783 0.335
0.609 -0.065 -0.791
0.220 -0.233 -0.947
-0.004 -0.910 -0.415
-0.511 0.627 -0.589
0.414 0.737 0.535
-0.679 0.139 -0.721
0.884 -0.296 0.362
0.262 0.432 0.863
0.088 0.185 -0.979
0.294 -0.907 0.302
0.887 -0.089 -0.453
0.257 -0.443 0.859
0.086 0.867 -0.491
0.863 0.504 -0.025
When I run this, I receive this error:
++ ver : 0.1 (libver : 0.3)
** ERROR: Cannot have a ragged cdiflist
Do you know how I can fix this issue? Is there a way to use dcm2niix_afni so that I don't need the cdiflist45 file or is this the current workaround?
Thanks!
Price
