Dear FSL experts,
I am using FSL 6.0.1, I ran topup in my data and I tried running eddy after, but I got an error which I can't seem to find referenced in the listserv.
Here is the command I ran:
eddy --imain=/Users/path/14_cmrr_mb3hydi_ipat2_64ch/output.nii --mask=/Users/path/topup_output/my_hifi_b0_Tcollapsed_brain_mask.nii.gz --acqp=/Users/path/acquisition_parameters.txt --index=/Users/path/index.txt --bvecs=/Users/path/14_cmrr_mb3hydi_ipat2_64ch/output.bvec --bvals=/Users/path/14_cmrr_mb3hydi_ipat2_64ch/output.bval --topup=/Users/path/topup_output/topup_output --json=/Users/path/14_cmrr_mb3hydi_ipat2_64ch/output.json --data_is_shelled --out=/Users/path/eddy_output/eddy_corrected_data
And here is the error message I got (I turned verbose on to make it clear at which stage the error occurred):
Reading images
Performing volume-to-volume registration
Running Register
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 0, Total mss = 50.7516
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 1, Total mss = 21.1202
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 2, Total mss = 19.9251
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 3, Total mss = 19.6102
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 4, Total mss = 19.3495
Running sm.ApplyB0LocationReference
Running sm.PolateB0MovPar
Running Register
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 2.615080
0.219281
0.535157
5.437753
4.977057
4.871069
4.992574
5.151094
Image Exception : #11 :: NEWIMAGE::raw_general_transform: vout and valid must have same dimensions
NEWIMAGE::raw_general_transform: vout and valid must have same dimensions
EDDY::: Eddy failed with message EDDY::: eddy.cpp::: EDDY::ReplacementManager *EDDY::DoVolumeToVolumeRegistration(const EDDY::EddyCommandLineOptions &, EDDY::ECScanManager &): Exception thrown
The only files created in my eddy_output folder which I set here --out=/Users/path/eddy_output/eddy_corrected_data
are called "eddy_corrected_data.eddy_values_of_all_input_parameters" and "eddy_corrected_data.eddy_command_txt". Nothing else is generated.
Any idea what the issue may be? I tried searching for this error but couldn't find anything.
Sincerely,
Nasia Metoki
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