Dear all, I've had some trouble feeding a flip angle map into mri_ms_fitparms. If I don't provide it, the estimates look fine; with the FA map however, all brain voxels in the resultant T1.mgz are set to 50000. I've checked that all images are registered, and the nominal values in the FA map look good to me. I'm running Freesurfer 5.1.0
Here's the output: johannes$ mri_ms_fitparms -afi B1Map_in_degrees.mgz DESPOT_FA_18.mgz DESPOT_FA_4.mgz t1_fs using flip angle map DESPOT1HIFI_B1Map_in_degrees.mgz with nominal value 60.0 degrees reading DESPOT_FA_18.mgz...TE = 3.70, TR = 8.00, flip angle = 18.00 reading DESPOT_FA_4.mgz...TE = 3.70, TR = 8.00, flip angle = 4.00 using 2 FLASH volumes to estimate tissue parameters. parameter rms = 77.083 non-equal flip_angle found for the volume 1. Flip_angle is set to zero. TR = 8.00, TE = 3.70, Flip_angle = 0.00 are used writing PD estimates to t1_fs/PD.mgz... writing T1 estimates to t1_fs/T1.mgz... writing residual sse to t1_fs/sse.mgz... writing faf map to t1_fs/faf.mgz... writing synthetic images to t1_fs/flash18.mgz... writing registration matrix to t1_fs/flash18.lta... writing synthetic images to t1_fs/flash4.mgz... writing registration matrix to t1_fs/flash4.lta... parameter estimation took 1 minutes and 18 seconds.
Any thoughts on what I'm doing wrong? Thanks for your help, Johannes