Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *************************************************************************** processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled *************************************************************************** processing subject 4168, 2 of 2... nn
Thank you in advance.