Hi, Thank you for the advice. I have a follow-up question. I seem to be getting a warning: non-equal flip_angle found for the volume 1. Flip_angle is set to zero. The full log is at the bottom. Using -------- freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_1_0 FSFAST_HOME /usr/local/freesurfer/stable5_1_0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/stable5_1_0/subjects MNI_DIR /usr/local/freesurfer/stable5_1_0/mni FSL_DIR /usr/pubsw/packages/fsl/current This data was collected at 7T. I have tried to use the AFI, but at 7T the range of flip angles is larger than the AFI can accurately map. Can you tell me some more about the warning? How does it figure out the flip angle is not equal? Is there a way to calculate what the flip angle was? My tissue is an agar phantom, which should be largely homogenous. I am trying to use either the PD or T1 estimates from mri_ms_fitparms to measure the temperature change in my agar phantom.
Thanks, Dan mri_ms_fitparms -afi afi_reg.mgz $F05/002/volume.mgz $F05/003/volume.mgz $F05/004/volume.mgz $F05/005/volume.mgz $F05/006/volume.mgz $F05/007/volume.mgz $F05/008/volume.mgz $F05/009/volume.mgz $F30/002/volume.mgz $F30/003/volume.mgz $F30/004/volume.mgz $F30/005/volume.mgz $F30/006/volume.mgz $F30/007/volume.mgz $F30/008/volume.mgz $F30/009/volume.mgz ./T1_12.13_afi/ using flip angle map afi_reg.mgz with nominal value 60.0 degrees reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//002/volume.mgz...TE = 1.67, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//003/volume.mgz...TE = 3.55, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//004/volume.mgz...TE = 5.43, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//005/volume.mgz...TE = 7.31, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//006/volume.mgz...TE = 9.19, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//007/volume.mgz...TE = 11.07, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//008/volume.mgz...TE = 12.95, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/012_gre_mgh_multiecho_05//009/volume.mgz...TE = 14.83, TR = 20.00, flip angle = 5.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//002/volume.mgz...TE = 1.67, TR = 20.00, flip angle = 30.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//003/volume.mgz...TE = 3.55, TR = 20.00, flip angle = 30.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//004/volume.mgz...TE = 5.43, TR = 20.00, flip angle = 30.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//005/volume.mgz...TE = 7.31, TR = 20.00, flip angle = 30.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//006/volume.mgz...TE = 9.19, TR = 20.00, flip angle = 30.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//007/volume.mgz...TE = 11.07, TR = 20.00, flip angle = 30.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//008/volume.mgz...TE = 12.95, TR = 20.00, flip angle = 30.00 reading /cluster/hbot/dwakeman/agario_p3_1nd/dcm/013_gre_mgh_multiecho_30//009/volume.mgz...TE = 14.83, TR = 20.00, flip angle = 30.00 using 2 FLASH volumes to estimate tissue parameters. parameter rms = 288.035 non-equal flip_angle found for the volume 1. Flip_angle is set to zero. TR = 20.00, TE = 1.67, Flip_angle = 0.00 are used writing PD estimates to ./T1_12.13_afi//PD.mgz... writing T1 estimates to ./T1_12.13_afi//T1.mgz... writing residual sse to ./T1_12.13_afi//sse.mgz... writing faf map to ./T1_12.13_afi//faf.mgz... writing synthetic images to ./T1_12.13_afi//flash5.mgz... writing registration matrix to ./T1_12.13_afi//flash5.lta... writing synthetic images to ./T1_12.13_afi//flash30.mgz... writing registration matrix to ./T1_12.13_afi//flash30.lta... estimating T2* with 2 different acquisitions, each with 8 echoes... writing T2star estimates to ./T1_12.13_afi//T2star.mgz... parameter estimation took 0 minutes and 56 seconds. On 10/10/12, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > you need to register them. > > cheers > Bruce > On Wed, 10 Oct 2012, dgw wrote: > >> Hi, >> >>> From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms), I >> can see that mri_ms_fitparms can accept and afi map. Can someone tell >> me what assumptions the -afi subcommand makes about the position of >> the afi map relative to the flash volumes? does it calculate >> everything in scanner coordinates, or do I need to register them to >> one another? >> >> Thanks, >> D >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
