domainname: Command not found. BIOC_0001_v01_FS /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula INFO: SUBJECTS_DIR is /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons INFO: Diffusion root is /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula Actual FREESURFER_HOME /Applications/freesurfer/7.2.0 trac-preproc -c /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/scripts/dmrirc.local -log /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/scripts/trac-all.log -cmd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/scripts/trac-all.cmd -no-isrunning -debug #------------------------------------- /Applications/freesurfer/7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Oct 18 16:56:34 +08 2022 rm -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/BIOC_0001_v01_DTI.nii /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/BIOC_0001_v01_DTI.nii /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz INFO: using NIfTI-1 qform reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/BIOC_0001_v01_DTI.nii... INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k TR=3600.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, -0.000400775, -0.0245065) j_ras = (-0.000400775, -0.999465, 0.0326939) k_ras = (-0.0245065, 0.0326939, 0.999165) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz... rm -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals.tmp /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvecs.tmp mv -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvecs.tmp /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvecs mv -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals.tmp /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals orientLAS /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 13.7114 mri_convert -oni 128 -onj 128 -onk 36 -oid -0.9997 -0.000400775 -0.0245065 -ojd 0.000400775 0.999465 -0.0326939 -okd -0.0245065 0.0326939 0.999165 -oc -0.856495 12.7796 -1.77656 -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 128 -onj 128 -onk 36 -oid -0.9997 -0.000400775 -0.0245065 -ojd 0.000400775 0.999465 -0.0326939 -okd -0.0245065 0.0326939 0.999165 -oc -0.856495 12.7796 -1.77656 -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.1.nii.gz normalizing out_i_direction: (-0.9997, -0.000400775, -0.0245065) -> (-0.9997, -0.000400775, -0.0245065) normalizing out_j_direction: (0.000400775, 0.999465, -0.0326939) -> (0.000400775, 0.999465, -0.0326939) reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz... TR=3600.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, -0.000400775, -0.0245065) j_ras = (-0.000400775, -0.999465, 0.0326939) k_ras = (-0.0245065, 0.0326939, 0.999165) Reslicing using nearest writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.1.nii.gz... INFO: found /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals, copying INFO: found /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.1.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.nii.gz mv -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.1.bvecs /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.bvecs mv -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.1.bvals /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.bvals eddy_correct /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz 0 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0000 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0001 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0002 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0003 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0004 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0005 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0006 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0007 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0008 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0009 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0010 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0011 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0012 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0013 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0014 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0015 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0016 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0017 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0018 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0019 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0020 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0021 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0022 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0023 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0024 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0025 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0026 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0027 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0028 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0029 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0030 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0031 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0032 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0033 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0034 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0035 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0036 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0037 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0038 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0039 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0040 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0041 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0042 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0043 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0044 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0045 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0046 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0047 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0048 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0049 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0050 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0051 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0052 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0053 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0054 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0055 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0056 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0057 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0058 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0059 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0060 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0061 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0062 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0063 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0064 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0065 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0066 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0067 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0068 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0069 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0070 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0071 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0072 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0073 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0074 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0075 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0076 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0077 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0078 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0079 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0080 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0081 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0082 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0083 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0084 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0085 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0086 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0087 processing 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/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0165 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0166 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0167 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0168 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0169 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0170 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0171 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0172 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0173 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0174 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0175 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0176 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0177 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0178 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0179 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0180 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0181 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0182 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0183 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0184 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0185 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0186 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0187 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0188 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0189 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0190 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0191 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0192 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0193 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0194 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0195 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0196 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0197 processing /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_tmp0198 xfmrot /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.ecclog /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.bvecs /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.bvecs cp -p /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.bvals /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.bvals mri_convert --in_like /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz mri_convert --in_like /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz reading info from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig_las.nii.gz... reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz... TR=3600.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, -0.000400775, -0.0245065) j_ras = (0.000400775, 0.999465, -0.0326939) k_ras = (-0.0245065, 0.0326939, 0.999165) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz... rm -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.full.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.bvecs.full /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.bvals.full mri_convert --frame 0 1 2 3 4 5 6 /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz mri_convert --frame 0 1 2 3 4 5 6 /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz... TR=3600.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, -0.000400775, -0.0245065) j_ras = (0.000400775, 0.999465, -0.0326939) k_ras = (-0.0245065, 0.0326939, 0.999165) keeping frames 0 1 2 3 4 5 6 writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz... mri_concat --i /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz --mean --o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 7 Allocing output Done allocing nframes = 7 Computing mean across frames Writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz bet /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb_brain.nii.gz -m -f 0.5 mv -f /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb_brain_mask.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff #------------------------------------- #@# DWI set selection Tue Oct 18 17:28:05 +08 2022 ln -sf dwi.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/data.nii.gz ln -sf dwi.bvecs /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/bvecs ln -sf dwi.bvals /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/bvals #------------------------------------- #@# Image quality assessment Tue Oct 18 17:28:05 +08 2022 /Applications/freesurfer/7.2.0/bin/dmri_motion --mat /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.ecclog --dwi /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz --bval /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals --T 358.285706 --out /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_motion.txt --outf /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_motion_byvol.txt 7.2.0 cwd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer cmdline /Applications/freesurfer/7.2.0/bin/dmri_motion --mat /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.ecclog --dwi /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz --bval /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals --T 358.285706 --out /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_motion.txt --outf /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_motion_byvol.txt sysname Darwin hostname Ashwatis-Mac-Studio.local machine x86_64 user ashwativipin Output motion measure file: /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_motion.txt Output frame-by-frame motion measure file: /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_motion_byvol.txt Input transform file: /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.ecclog Input DWI file(s): /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz Input b-value table(s): /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals Low-b image intensity threshold: 358.286 Nominal diffusivity: 0.001 Loading DWI volume series from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz Loading b-value table from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.bvals Computing within-volume head motion measures Loading volume-to-baseline affine transformations Computing between-volume head motion measures INFO: Processed transforms for 199 volumes Done in 4.497 sec. dmri_motion done #------------------------------------- #@# Intra-subject registration Tue Oct 18 17:28:10 +08 2022 bbregister --s BIOC_0001_v01_FS --init-fsl --dti --9 --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta tmp /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029 Log file is /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.log Tue Oct 18 17:28:10 +08 2022 setenv SUBJECTS_DIR /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons cd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer /Applications/freesurfer/7.2.0/bin/bbregister --s BIOC_0001_v01_FS --init-fsl --dti --9 --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta FreeSurferEnv.csh 7.2.0 Darwin Ashwatis-Mac-Studio.local 21.4.0 Darwin Kernel Version 21.4.0: Fri Mar 18 00:46:32 PDT 2022; root:xnu-8020.101.4~15/RELEASE_ARM64_T6000 arm64 FREESURFER_HOME /Applications/freesurfer/7.2.0 mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz... TR=3600.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, -0.000400775, -0.0245065) j_ras = (0.000400775, 0.999465, -0.0326939) k_ras = (-0.0245065, 0.0326939, 0.999165) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii... fslregister --s BIOC_0001_v01_FS --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat --niters 1 --maxangle 90 --tmp /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat.fslregister.log Tue Oct 18 17:28:10 +08 2022 --s BIOC_0001_v01_FS --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat --niters 1 --maxangle 90 --tmp /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov FreeSurferEnv.csh 7.2.0 Ashwatis-Mac-Studio.local Darwin Ashwatis-Mac-Studio.local 21.4.0 Darwin Kernel Version 21.4.0: Fri Mar 18 00:46:32 PDT 2022; root:xnu-8020.101.4~15/RELEASE_ARM64_T6000 arm64 nIters 1 -------------------------------------- /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/brainmask.mgz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/refvol.fslregister.nii mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/brainmask.mgz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/refvol.fslregister.nii reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -9.31323e-10) j_ras = (0, -1.15688e-08, -1) k_ras = (0, 1, -2.91038e-09) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/refvol.fslregister.nii... -------------------------------------- /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii --frame 0 mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii --frame 0 reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii... TR=3600.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, -0.000400775, -0.0245065) j_ras = (0.000400775, 0.999465, -0.0326939) k_ras = (-0.0245065, 0.0326939, 0.999165) keeping frame 0 writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii... Mov determinant is -13.7114 /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer tkregister2_cmdl --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/reg0.74078.dat --targ brainmask --fstarg --regheader --fslregout /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat.fsl.mat0 --s BIOC_0001_v01_FS --noedit target volume brainmask movable volume /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii reg file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/reg0.74078.dat LoadVol 0 ZeroCRAS 0 7.2.0 Diagnostic Level -1 INFO: loading target /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/brainmask.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.87500 0.00000 0.00000 120.00000; 0.00000 0.00000 3.90014 -70.20248; 0.00000 -1.87500 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.99970 0.00040 0.02451 -1.15370; -0.02451 0.03269 0.99916 -29.16957; -0.00040 -0.99947 0.03269 -6.65186; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99970 0.00040 0.02451 -1.15370; -0.02451 0.03269 0.99916 -29.16957; -0.00040 -0.99947 0.03269 -6.65186; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = BIOC_0001_v01_FS RegMat --------------------------- 0.99970 0.00040 0.02451 -1.15370; -0.02451 0.03269 0.99916 -29.16957; -0.00040 -0.99947 0.03269 -6.65186; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -13.7114, ref det = -1 Tue Oct 18 17:28:11 +08 2022 /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer flirt.fsl -ref /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/refvol.fslregister.nii -in /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/fslmat0.trans.mat -schedule /Applications/freesurfer/7.2.0/bin/fsl.5.0.2.xyztrans.sch -init /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat.fsl.mat0 Tue Oct 18 17:28:16 +08 2022 /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer flirt.fsl -ref /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/refvol.fslregister.nii -in /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat.fsl.mat -init /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/fslregister/fslmat0.trans.mat -schedule /Applications/freesurfer/7.2.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s BIOC_0001_v01_FS --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --targ brainmask --fstarg --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat --fslreg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat.fsl.mat --noedit ---- FSL registration matrix -------- 0.99951 0.00313 0.03129 5.14361; 0.03120 0.02449 -0.99921 166.09880; -0.00389 0.99970 0.02438 0.76005; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- target volume brainmask movable volume /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii reg file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat LoadVol 0 ZeroCRAS 0 7.2.0 Diagnostic Level -1 INFO: loading target /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/brainmask.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii Tmov: -------------------- -1.87500 0.00000 0.00000 120.00000; 0.00000 0.00000 3.90014 -70.20248; 0.00000 -1.87500 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -13.7114, ref det = -1 ---- Input registration matrix (computed) -------- 0.99951 0.00389 0.03120 -1.11172; -0.03129 0.02438 0.99921 -25.18750; 0.00313 -0.99969 0.02449 -6.65231; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99951 0.00389 0.03120 -1.11172; -0.03129 0.02438 0.99921 -25.18750; 0.00313 -0.99969 0.02449 -6.65231; 0.00000 0.00000 0.00000 1.00000; Determinant 0.999999 subject = BIOC_0001_v01_FS RegMat --------------------------- 0.99951 0.00389 0.03120 -1.11172; -0.03129 0.02438 0.99921 -25.18750; 0.00313 -0.99969 0.02449 -6.65231; 0.00000 0.00000 0.00000 1.00000; (standard_in) 1: illegal character: I (standard_in) 1: illegal character: O (standard_in) 1: parse error (standard_in) 1: illegal character: _ (standard_in) 1: illegal character: _ (standard_in) 1: illegal character: S Started at Tue Oct 18 17:28:10 +08 2022 Ended at Tue Oct 18 17:28:28 +08 2022 fslregister Done To check results, run: tkregisterfv --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat --surf orig mri_segreg --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --init-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat --out-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.2.0 setenv SUBJECTS_DIR /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons cd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer mri_segreg --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --init-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat --out-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname Ashwatis-Mac-Studio.local machine x86_64 user ashwativipin movvol /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii regfile /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.init.dat subject BIOC_0001_v01_FS dof 6 outregfile /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1666402401 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99951 0.00389 0.03120 -1.11172; -0.03129 0.02438 0.99921 -25.18750; 0.00313 -0.99969 0.02449 -6.65231; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.021802 1 -25.0 -25.0 25.0 0.978900 2 -25.0 25.0 -25.0 1.015496 3 -25.0 25.0 25.0 1.051933 4 25.0 -25.0 -25.0 1.005140 5 25.0 -25.0 25.0 1.015201 6 25.0 25.0 -25.0 1.028726 7 25.0 25.0 25.0 0.975171 REL: 8 0.480621 8.092369 1.011546 rel = 0.475135 Initial costs ---------------- Number of surface hits 2559 WM Intensity 449.5019 +/- 89.6409 Ctx Intensity 519.1970 +/- 127.2672 Pct Contrast 13.1528 +/- 20.2820 Cost 0.4806 RelCost 0.4751 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9738 0.9738 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9738 0.9738 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9243 0.9243 0.0 12 -4.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.9122 0.9122 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8380 0.8380 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8366 0.8366 0.0 24 -4.0000 -4.0000 -4.0000 4.0000 4.0000 -4.0000 0.8328 0.8328 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8134 0.8134 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7131 0.7131 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.5725 0.5725 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.3192 0.3192 0.0 Brute Force -------------------------- Min cost was 0.319156 Number of iterations 729 Search time 1.120108 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.319156 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.3183062633 7 0.206 -4.000 0.000 0.000 0.000 0.000 0.3117802182 8 0.197 -4.000 0.000 0.000 0.000 0.000 0.3116353039 10 0.174 -4.000 0.000 0.000 0.000 0.000 0.3115915618 11 0.183 -4.000 0.000 0.000 0.000 0.000 0.3115627418 15 0.183 -3.000 0.000 0.000 0.000 0.000 0.2197359808 18 0.183 -2.382 0.000 0.000 0.000 0.000 0.2121286230 21 0.183 -2.466 0.000 0.000 0.000 0.000 0.2110191907 23 0.183 -2.455 0.000 0.000 0.000 0.000 0.2109825472 25 0.183 -2.454 0.000 0.000 0.000 0.000 0.2109814660 26 0.183 -2.453 0.000 0.000 0.000 0.000 0.2109808780 32 0.183 -2.453 0.382 0.000 0.000 0.000 0.2005823197 35 0.183 -2.453 0.489 0.000 0.000 0.000 0.1999765901 36 0.183 -2.453 0.460 0.000 0.000 0.000 0.1997277856 37 0.183 -2.453 0.451 0.000 0.000 0.000 0.1997176668 38 0.183 -2.453 0.453 0.000 0.000 0.000 0.1997175001 44 0.183 -2.453 0.453 -0.618 0.000 0.000 0.1924830515 46 0.183 -2.453 0.453 -0.422 0.000 0.000 0.1888109766 50 0.183 -2.453 0.453 -0.451 0.000 0.000 0.1887758021 51 0.183 -2.453 0.453 -0.447 0.000 0.000 0.1887735955 52 0.183 -2.453 0.453 -0.444 0.000 0.000 0.1887727208 54 0.183 -2.453 0.453 -0.445 0.000 0.000 0.1887725658 62 0.183 -2.453 0.453 -0.445 -0.139 0.000 0.1841018469 63 0.183 -2.453 0.453 -0.445 -0.203 0.000 0.1822931772 65 0.183 -2.453 0.453 -0.445 -0.236 0.000 0.1821583798 66 0.183 -2.453 0.453 -0.445 -0.228 0.000 0.1821506537 70 0.183 -2.453 0.453 -0.445 -0.227 0.000 0.1821505431 78 0.183 -2.453 0.453 -0.445 -0.227 -0.194 0.1815103209 79 0.183 -2.453 0.453 -0.445 -0.227 -0.125 0.1813363060 80 0.183 -2.453 0.453 -0.445 -0.227 -0.132 0.1813185160 powell nthiter 1: fret = 0.181319 92 0.161 -2.453 0.453 -0.445 -0.227 -0.132 0.1812458352 94 0.167 -2.453 0.453 -0.445 -0.227 -0.132 0.1812329907 96 0.168 -2.453 0.453 -0.445 -0.227 -0.132 0.1812323015 97 0.169 -2.453 0.453 -0.445 -0.227 -0.132 0.1812322627 106 0.169 -2.457 0.453 -0.445 -0.227 -0.132 0.1812237124 107 0.169 -2.465 0.453 -0.445 -0.227 -0.132 0.1812203290 108 0.169 -2.463 0.453 -0.445 -0.227 -0.132 0.1812198289 116 0.169 -2.463 0.612 -0.445 -0.227 -0.132 0.1786880658 119 0.169 -2.463 0.624 -0.445 -0.227 -0.132 0.1786793998 120 0.169 -2.463 0.619 -0.445 -0.227 -0.132 0.1786701479 121 0.169 -2.463 0.618 -0.445 -0.227 -0.132 0.1786693880 129 0.169 -2.463 0.618 -0.549 -0.227 -0.132 0.1783664707 130 0.169 -2.463 0.618 -0.514 -0.227 -0.132 0.1783102577 133 0.169 -2.463 0.618 -0.503 -0.227 -0.132 0.1782940783 135 0.169 -2.463 0.618 -0.504 -0.227 -0.132 0.1782931786 137 0.169 -2.463 0.618 -0.505 -0.227 -0.132 0.1782925822 145 0.169 -2.463 0.618 -0.505 -0.169 -0.132 0.1778918819 146 0.169 -2.463 0.618 -0.505 -0.163 -0.132 0.1778858727 148 0.169 -2.463 0.618 -0.505 -0.164 -0.132 0.1778856067 158 0.169 -2.463 0.618 -0.505 -0.164 -0.133 0.1778801848 159 0.169 -2.463 0.618 -0.505 -0.164 -0.148 0.1778389495 162 0.169 -2.463 0.618 -0.505 -0.164 -0.147 0.1778381595 166 0.156 -2.473 0.783 -0.566 -0.101 -0.162 0.1764888017 174 0.156 -2.473 0.774 -0.562 -0.104 -0.161 0.1764776426 176 0.156 -2.473 0.774 -0.562 -0.104 -0.161 0.1764775395 180 0.156 -2.473 0.774 -0.562 -0.104 -0.161 0.1764774017 powell nthiter 2: fret = 0.176477 188 0.118 -2.473 0.774 -0.562 -0.104 -0.161 0.1762179217 189 0.117 -2.473 0.774 -0.562 -0.104 -0.161 0.1762169074 191 0.116 -2.473 0.774 -0.562 -0.104 -0.161 0.1762164596 199 0.116 -2.459 0.774 -0.562 -0.104 -0.161 0.1762014807 208 0.116 -2.459 0.774 -0.562 -0.104 -0.262 0.1760947495 209 0.116 -2.459 0.774 -0.562 -0.104 -0.218 0.1759166193 211 0.116 -2.459 0.774 -0.562 -0.104 -0.224 0.1759124864 213 0.116 -2.459 0.774 -0.562 -0.104 -0.223 0.1759124836 221 0.116 -2.459 0.774 -0.638 -0.104 -0.223 0.1754040194 222 0.116 -2.459 0.774 -0.649 -0.104 -0.223 0.1753834051 224 0.116 -2.459 0.774 -0.654 -0.104 -0.223 0.1753787468 225 0.116 -2.459 0.774 -0.655 -0.104 -0.223 0.1753783721 226 0.116 -2.459 0.774 -0.656 -0.104 -0.223 0.1753777692 234 0.116 -2.459 0.774 -0.656 -0.142 -0.223 0.1750909431 236 0.116 -2.459 0.774 -0.656 -0.134 -0.223 0.1750570284 238 0.116 -2.459 0.774 -0.656 -0.133 -0.223 0.1750558744 239 0.116 -2.459 0.774 -0.656 -0.132 -0.223 0.1750557365 248 0.116 -2.459 0.774 -0.656 -0.132 -0.223 0.1750556520 249 0.116 -2.459 0.774 -0.656 -0.132 -0.223 0.1750555494 250 0.116 -2.459 0.774 -0.656 -0.132 -0.223 0.1750554562 powell nthiter 3: fret = 0.175055 260 0.088 -2.459 0.774 -0.656 -0.132 -0.223 0.1749161578 261 0.087 -2.459 0.774 -0.656 -0.132 -0.223 0.1749160843 269 0.087 -2.586 0.774 -0.656 -0.132 -0.223 0.1745619131 270 0.087 -2.551 0.774 -0.656 -0.132 -0.223 0.1744847197 271 0.087 -2.548 0.774 -0.656 -0.132 -0.223 0.1744838825 282 0.087 -2.548 0.774 -0.656 -0.132 -0.213 0.1744648435 283 0.087 -2.548 0.774 -0.656 -0.132 -0.212 0.1744647248 291 0.087 -2.548 0.774 -0.692 -0.132 -0.212 0.1743368179 293 0.087 -2.548 0.774 -0.690 -0.132 -0.212 0.1743364398 304 0.087 -2.548 0.774 -0.690 -0.126 -0.212 0.1743223654 305 0.087 -2.548 0.774 -0.690 -0.125 -0.212 0.1743219457 315 0.087 -2.548 0.775 -0.690 -0.125 -0.212 0.1743216171 317 0.087 -2.548 0.776 -0.691 -0.125 -0.212 0.1743215511 318 0.087 -2.548 0.776 -0.691 -0.125 -0.212 0.1743214915 powell nthiter 4: fret = 0.174321 328 0.076 -2.548 0.776 -0.691 -0.125 -0.212 0.1743043920 330 0.079 -2.548 0.776 -0.691 -0.125 -0.212 0.1743032663 341 0.079 -2.565 0.776 -0.691 -0.125 -0.212 0.1742765671 342 0.079 -2.567 0.776 -0.691 -0.125 -0.212 0.1742762544 360 0.079 -2.567 0.776 -0.708 -0.125 -0.212 0.1742744581 361 0.079 -2.567 0.776 -0.700 -0.125 -0.212 0.1742669384 362 0.079 -2.567 0.776 -0.699 -0.125 -0.212 0.1742669379 372 0.079 -2.567 0.776 -0.699 -0.124 -0.212 0.1742666518 387 0.070 -2.586 0.776 -0.707 -0.123 -0.212 0.1742532009 392 0.065 -2.598 0.776 -0.712 -0.122 -0.212 0.1742511182 396 0.065 -2.599 0.776 -0.712 -0.122 -0.212 0.1742509517 400 0.065 -2.599 0.776 -0.712 -0.122 -0.212 0.1742509224 powell nthiter 5: fret = 0.174251 410 0.048 -2.599 0.776 -0.712 -0.122 -0.212 0.1742412045 411 0.054 -2.599 0.776 -0.712 -0.122 -0.212 0.1742252600 412 0.056 -2.599 0.776 -0.712 -0.122 -0.212 0.1742245070 420 0.055 -2.599 0.780 -0.714 -0.120 -0.212 0.1742199823 421 0.055 -2.599 0.781 -0.714 -0.120 -0.212 0.1742198962 432 0.055 -2.599 0.781 -0.714 -0.120 -0.219 0.1742169211 433 0.055 -2.599 0.781 -0.714 -0.120 -0.218 0.1742160104 434 0.055 -2.599 0.781 -0.714 -0.120 -0.217 0.1742156134 444 0.055 -2.599 0.781 -0.716 -0.120 -0.217 0.1742148964 456 0.055 -2.599 0.781 -0.716 -0.124 -0.217 0.1742108975 465 0.055 -2.600 0.781 -0.717 -0.123 -0.217 0.1742107192 466 0.055 -2.601 0.781 -0.717 -0.123 -0.217 0.1742105705 powell nthiter 6: fret = 0.174211 483 0.054 -2.601 0.781 -0.717 -0.123 -0.217 0.1742097475 484 0.052 -2.601 0.781 -0.717 -0.123 -0.217 0.1742096363 493 0.052 -2.601 0.784 -0.718 -0.122 -0.217 0.1742085830 496 0.052 -2.601 0.784 -0.718 -0.122 -0.217 0.1742084107 507 0.052 -2.601 0.784 -0.718 -0.122 -0.223 0.1742035422 518 0.052 -2.601 0.784 -0.719 -0.122 -0.223 0.1742034523 528 0.052 -2.601 0.784 -0.719 -0.123 -0.223 0.1742033349 535 0.049 -2.608 0.784 -0.722 -0.123 -0.223 0.1741960435 537 0.048 -2.609 0.784 -0.723 -0.123 -0.223 0.1741956131 541 0.048 -2.609 0.784 -0.723 -0.123 -0.223 0.1741956121 542 0.048 -2.609 0.784 -0.723 -0.123 -0.223 0.1741955987 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.002089 1 -25.0 -25.0 25.0 1.001641 2 -25.0 25.0 -25.0 0.995086 3 -25.0 25.0 25.0 1.036456 4 25.0 -25.0 -25.0 1.008167 5 25.0 -25.0 25.0 1.043223 6 25.0 25.0 -25.0 1.034195 7 25.0 25.0 25.0 0.982561 REL: 8 0.174196 8.103420 1.012927 rel = 0.171972 Number of iterations 6 Min cost was 0.174196 Number of FunctionCalls 545 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.846402 sec Parameters at optimum (transmm) 0.04828 -2.60922 0.78416 Parameters at optimum (rotdeg) -0.72272 -0.12275 -0.22273 Final costs ---------------- Number of surface hits 2559 WM Intensity 419.8031 +/- 71.1306 Ctx Intensity 505.9951 +/- 93.5859 Pct Contrast 18.0582 +/- 15.8384 Cost 0.1742 RelCost 0.4751 Reg at min cost was 0.99937 0.00608 0.03506 -1.14810; -0.03513 0.01175 0.99931 -27.87417; 0.00566 -0.99991 0.01195 -5.55229; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/bbr.pass1.dat, type = 14 Original Reg 0.99951 0.00389 0.03120 -1.11172; -0.03129 0.02438 0.99921 -25.18750; 0.00313 -0.99969 0.02449 -6.65231; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00014 -0.00219 -0.00386 0.03637; 0.00384 0.01264 -0.00010 2.68667; -0.00254 0.00022 0.01254 -1.10003; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.393876 Computing change in rh position Surface-RMS-Diff-mm 2.513548 0.499466 3.682196 mri_segreg done mri_segreg --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --init-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/bbr.pass1.dat --out-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 9 --nmax 36 --param /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.2.0 setenv SUBJECTS_DIR /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons cd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer mri_segreg --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii --init-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/bbr.pass1.dat --out-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 9 --nmax 36 --param /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname Ashwatis-Mac-Studio.local machine x86_64 user ashwativipin movvol /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/template.nii regfile /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/tmp.bbregister.74029/bbr.pass1.dat subject BIOC_0001_v01_FS dof 9 outregfile /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1666105603 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99937 0.00608 0.03506 -1.14810; -0.03513 0.01175 0.99931 -27.87417; 0.00566 -0.99991 0.01195 -5.55229; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.002752 1 -25.0 -25.0 25.0 0.989412 2 -25.0 25.0 -25.0 1.007631 3 -25.0 25.0 25.0 1.030108 4 25.0 -25.0 -25.0 0.989267 5 25.0 -25.0 25.0 1.000204 6 25.0 25.0 -25.0 1.001224 7 25.0 25.0 25.0 0.989808 REL: 8 0.173533 8.010405 1.001301 rel = 0.173308 Initial costs ---------------- Number of surface hits 257103 WM Intensity 420.3383 +/- 70.1178 Ctx Intensity 506.3215 +/- 91.9150 Pct Contrast 18.0216 +/- 15.7227 Cost 0.1735 RelCost 0.1733 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1812 0.1812 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1780 0.1780 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1779 0.1779 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.1774 0.1774 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1767 0.1767 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.1756 0.1756 0.0 273 0.0000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1752 0.1752 0.0 282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1750 0.1750 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1748 0.1748 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1742 0.1742 0.0 Brute Force -------------------------- Min cost was 0.174196 Number of iterations 729 Search time 1.026949 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 9 0 0 1 0 2 0 3 0 4 0 5 0 6 1 7 1 8 1 fs_powell::minimize nparams 9 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.173533 7 0.065 0.000 0.000 0.000 0.000 0.000 sc: 1.000 1.000 1.000 0.1730578373 25 0.066 0.000 0.014 0.000 0.000 0.000 sc: 1.000 1.000 1.000 0.1730160157 26 0.066 0.000 0.026 0.000 0.000 0.000 sc: 1.000 1.000 1.000 0.1730009316 27 0.066 0.000 0.030 0.000 0.000 0.000 sc: 1.000 1.000 1.000 0.1729999731 28 0.066 0.000 0.031 0.000 0.000 0.000 sc: 1.000 1.000 1.000 0.1729999011 36 0.066 0.000 0.031 0.153 0.000 0.000 sc: 1.000 1.000 1.000 0.1715507672 37 0.066 0.000 0.031 0.155 0.000 0.000 sc: 1.000 1.000 1.000 0.1715489744 38 0.066 0.000 0.031 0.163 0.000 0.000 sc: 1.000 1.000 1.000 0.1715470062 40 0.066 0.000 0.031 0.161 0.000 0.000 sc: 1.000 1.000 1.000 0.1715468485 49 0.066 0.000 0.031 0.161 0.045 0.000 sc: 1.000 1.000 1.000 0.1713888435 59 0.066 0.000 0.031 0.161 0.045 -0.114 sc: 1.000 1.000 1.000 0.1705771202 73 0.066 0.000 0.031 0.161 0.045 -0.114 sc: 1.001 1.000 1.000 0.1704725193 84 0.066 0.000 0.031 0.161 0.045 -0.114 sc: 1.001 0.996 1.000 0.1704310074 86 0.066 0.000 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 1.000 0.1703231864 98 0.066 0.000 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 0.991 0.1620065051 99 0.066 0.000 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1613349162 powell nthiter 1: fret = 0.161335 108 0.012 0.000 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1608315284 110 0.002 0.000 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1608205918 119 0.002 0.072 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1605424910 120 0.002 0.071 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1605421018 121 0.002 0.068 0.031 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1605416709 131 0.002 0.068 0.168 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1593306619 132 0.002 0.068 0.164 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1593278964 133 0.002 0.068 0.161 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1593274927 134 0.002 0.068 0.162 0.161 0.045 -0.114 sc: 1.001 0.998 0.992 0.1593273639 142 0.002 0.068 0.162 0.198 0.045 -0.114 sc: 1.001 0.998 0.992 0.1592450116 144 0.002 0.068 0.162 0.197 0.045 -0.114 sc: 1.001 0.998 0.992 0.1592449452 154 0.002 0.068 0.162 0.197 0.056 -0.114 sc: 1.001 0.998 0.992 0.1592279867 155 0.002 0.068 0.162 0.197 0.057 -0.114 sc: 1.001 0.998 0.992 0.1592278330 163 0.002 0.068 0.162 0.197 0.057 -0.149 sc: 1.001 0.998 0.992 0.1592270523 164 0.002 0.068 0.162 0.197 0.057 -0.131 sc: 1.001 0.998 0.992 0.1592104190 188 0.002 0.068 0.162 0.197 0.057 -0.131 sc: 1.001 0.994 0.992 0.1590605999 189 0.002 0.068 0.162 0.197 0.057 -0.131 sc: 1.001 0.995 0.992 0.1589686299 201 0.002 0.068 0.162 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1582511308 203 -0.061 0.136 0.293 0.233 0.069 -0.149 sc: 1.001 0.993 0.988 0.1582098625 powell nthiter 2: fret = 0.158251 222 -0.008 0.112 0.162 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1581458362 223 -0.008 0.109 0.162 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1581447101 224 -0.008 0.107 0.162 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1581441675 225 -0.008 0.106 0.162 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1581441635 233 -0.008 0.106 0.224 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1579230845 234 -0.008 0.106 0.219 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1579189440 235 -0.008 0.106 0.216 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1579179473 236 -0.008 0.106 0.215 0.197 0.057 -0.131 sc: 1.001 0.995 0.990 0.1579179238 244 -0.008 0.106 0.215 0.202 0.057 -0.131 sc: 1.001 0.995 0.990 0.1579174882 245 -0.008 0.106 0.215 0.200 0.057 -0.131 sc: 1.001 0.995 0.990 0.1579173874 254 -0.008 0.106 0.215 0.200 0.065 -0.131 sc: 1.001 0.995 0.990 0.1579084385 255 -0.008 0.106 0.215 0.200 0.066 -0.131 sc: 1.001 0.995 0.990 0.1579081759 265 -0.008 0.106 0.215 0.200 0.066 -0.130 sc: 1.001 0.995 0.990 0.1579080826 277 -0.008 0.106 0.215 0.200 0.066 -0.130 sc: 1.000 0.995 0.990 0.1579016889 powell nthiter 3: fret = 0.157902 310 -0.014 0.106 0.215 0.200 0.066 -0.130 sc: 1.000 0.995 0.990 0.1579004063 311 -0.012 0.106 0.215 0.200 0.066 -0.130 sc: 1.000 0.995 0.990 0.1579000671 320 -0.012 0.111 0.215 0.200 0.066 -0.130 sc: 1.000 0.995 0.990 0.1578983296 330 -0.012 0.111 0.223 0.200 0.066 -0.130 sc: 1.000 0.995 0.990 0.1578931455 340 -0.012 0.111 0.223 0.199 0.066 -0.130 sc: 1.000 0.995 0.990 0.1578930749 351 -0.012 0.111 0.223 0.199 0.063 -0.130 sc: 1.000 0.995 0.990 0.1578917135 352 -0.012 0.111 0.223 0.199 0.062 -0.130 sc: 1.000 0.995 0.990 0.1578917030 361 -0.012 0.111 0.223 0.199 0.062 -0.140 sc: 1.000 0.995 0.990 0.1578867299 363 -0.012 0.111 0.223 0.199 0.062 -0.141 sc: 1.000 0.995 0.990 0.1578867149 399 -0.012 0.111 0.223 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1578486797 powell nthiter 4: fret = 0.157849 409 -0.018 0.111 0.223 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1578480505 410 -0.015 0.111 0.223 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1578474575 419 -0.015 0.110 0.223 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1578461119 420 -0.015 0.100 0.223 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1578415698 429 -0.015 0.100 0.267 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1577519849 430 -0.015 0.100 0.260 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1577467846 431 -0.015 0.100 0.258 0.199 0.062 -0.141 sc: 1.000 0.995 0.989 0.1577462768 440 -0.015 0.100 0.258 0.194 0.062 -0.141 sc: 1.000 0.995 0.989 0.1577412044 441 -0.015 0.100 0.258 0.187 0.062 -0.141 sc: 1.000 0.995 0.989 0.1577394634 442 -0.015 0.100 0.258 0.189 0.062 -0.141 sc: 1.000 0.995 0.989 0.1577391437 451 -0.015 0.100 0.258 0.189 0.065 -0.141 sc: 1.000 0.995 0.989 0.1577358227 452 -0.015 0.100 0.258 0.189 0.067 -0.141 sc: 1.000 0.995 0.989 0.1577355007 461 -0.015 0.100 0.258 0.189 0.067 -0.137 sc: 1.000 0.995 0.989 0.1577347920 463 -0.015 0.100 0.258 0.189 0.067 -0.136 sc: 1.000 0.995 0.989 0.1577347911 489 -0.015 0.100 0.258 0.189 0.067 -0.136 sc: 1.000 0.994 0.989 0.1577098183 powell nthiter 5: fret = 0.157710 510 -0.019 0.100 0.258 0.189 0.067 -0.136 sc: 1.000 0.994 0.989 0.1577092847 511 -0.018 0.100 0.258 0.189 0.067 -0.136 sc: 1.000 0.994 0.989 0.1577092183 520 -0.018 0.107 0.258 0.189 0.067 -0.136 sc: 1.000 0.994 0.989 0.1577066129 530 -0.018 0.107 0.263 0.189 0.067 -0.136 sc: 1.000 0.994 0.989 0.1577045807 540 -0.018 0.107 0.263 0.183 0.067 -0.136 sc: 1.000 0.994 0.989 0.1577031307 542 -0.018 0.107 0.263 0.184 0.067 -0.136 sc: 1.000 0.994 0.989 0.1577029582 552 -0.018 0.107 0.263 0.184 0.068 -0.136 sc: 1.000 0.994 0.989 0.1577028459 562 -0.018 0.107 0.263 0.184 0.068 -0.135 sc: 1.000 0.994 0.989 0.1577026191 563 -0.018 0.107 0.263 0.184 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577025017 powell nthiter 6: fret = 0.157703 618 -0.018 0.106 0.263 0.184 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577024335 627 -0.018 0.106 0.265 0.184 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577019394 636 -0.018 0.106 0.265 0.182 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577019193 638 -0.018 0.106 0.265 0.183 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577018130 698 -0.018 0.105 0.266 0.182 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577017755 702 -0.018 0.105 0.265 0.183 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577017754 706 -0.018 0.105 0.265 0.183 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577017728 707 -0.018 0.105 0.265 0.183 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577017695 powell nthiter 7: fret = 0.157702 727 -0.018 0.106 0.265 0.183 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577017615 796 -0.018 0.106 0.266 0.182 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577016796 797 -0.018 0.105 0.266 0.182 0.068 -0.133 sc: 1.000 0.994 0.989 0.1577016781 powell nthiter 8: fret = 0.157702 854 -0.018 0.105 0.266 0.182 0.069 -0.133 sc: 1.000 0.994 0.989 0.1577016680 Powell done niters = 8 Computing relative cost 0 -25.0 -25.0 -25.0 1.002852 1 -25.0 -25.0 25.0 0.990547 2 -25.0 25.0 -25.0 1.009239 3 -25.0 25.0 25.0 1.031052 4 25.0 -25.0 -25.0 0.991111 5 25.0 -25.0 25.0 0.999936 6 25.0 25.0 -25.0 1.002410 7 25.0 25.0 25.0 0.986170 REL: 8 0.157702 8.013316 1.001664 rel = 0.15744 Number of iterations 8 Min cost was 0.157702 Number of FunctionCalls 899 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 74.322493 sec Parameters at optimum (transmm) -0.01787 0.10541 0.26624 Parameters at optimum (rotdeg) 0.18207 0.06927 -0.13313 Parameters at optimum (scale) 1.00000 0.99420 0.98937 Final costs ---------------- Number of surface hits 257103 WM Intensity 418.6333 +/- 68.2256 Ctx Intensity 504.4845 +/- 87.4054 Pct Contrast 18.1724 +/- 14.5067 Cost 0.1577 RelCost 0.1733 Reg at min cost was 0.99929 0.00491 0.03740 -1.23751; -0.03725 0.01483 0.99339 -27.58731; 0.00430 -0.98925 0.01492 -5.31607; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat, type = 14 Original Reg 0.99937 0.00608 0.03506 -1.14810; -0.03513 0.01175 0.99931 -27.87417; 0.00566 -0.99991 0.01195 -5.55229; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00008 0.00117 -0.00234 0.08941; 0.00212 -0.00308 0.00592 -0.28686; 0.00137 -0.01067 -0.00297 -0.23622; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.450226 Computing change in rh position Surface-RMS-Diff-mm 0.436093 0.223544 1.110349 mri_segreg done MinCost: 0.157702 418.633269 504.484517 18.172409 tkregister2_cmdl --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat --noedit --ltaout /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz reg file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.dat LoadVol 0 ZeroCRAS 0 7.2.0 Diagnostic Level -1 ---- Input registration matrix -------- 0.99929 0.00491 0.03740 -1.23751; -0.03725 0.01483 0.99339 -27.58731; 0.00430 -0.98925 0.01492 -5.31607; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz Tmov: -------------------- -1.87500 0.00000 0.00000 120.00000; 0.00000 0.00000 3.90014 -70.20248; 0.00000 -1.87500 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99929 0.00491 0.03740 -1.23751; -0.03725 0.01483 0.99339 -27.58731; 0.00430 -0.98925 0.01492 -5.31607; 0.00000 0.00000 0.00000 1.00000; Determinant 0.983629 subject = BIOC_0001_v01_FS RegMat --------------------------- 0.99929 0.00491 0.03740 -1.23751; -0.03725 0.01483 0.99339 -27.58731; 0.00430 -0.98925 0.01492 -5.31607; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Oct 18 17:28:10 +08 2022 Ended at Tue Oct 18 17:29:54 +08 2022 BBR-Run-Time-Sec 104 bbregister Done To check results, run: tkregisterfv --mov /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/lowb.nii.gz --reg /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta --surfs --sd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons lta_convert --inlta /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta --invert --outlta /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta 7.2.0 --inlta: /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta input LTA transform. --invert: will invert transform. --outlta: /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta output LTA. LTA read, type : 1 0.99991 -0.00522 -0.01303 -0.17215; 0.00494 1.01057 -0.01793 0.57871; 0.01275 0.01763 1.00559 -1.74249; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... lta_convert successful. mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -9.31323e-10) j_ras = (0, -1.15688e-08, -1) k_ras = (0, 1, -2.91038e-09) MRIcopyHeader(): source has ctab writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz... mri_binarize --i /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz 7.2.0 cwd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer cmdline mri_binarize --i /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz sysname Darwin hostname Ashwatis-Mac-Studio.local machine x86_64 user ashwativipin input /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz frame 0 nErode3d 2 nErode2d 0 output /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 1199535 values in range Dilating 4 voxels in 3d Eroding 2 voxels in 3d Counting number of voxels in first frame Found 1601532 voxels in final mask Writing output to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz Count: 1601532 1601532.000000 16777216 9.545875 mri_binarize done mri_binarize --i /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter.nii.gz 7.2.0 cwd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer cmdline mri_binarize --i /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter.nii.gz sysname Darwin hostname Ashwatis-Mac-Studio.local machine x86_64 user ashwativipin input /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 7 0 2 1 41 2 7 3 46 4 172 5 177 6 77 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 MRIcopyHeader(): source has ctab Starting parallel 1 Found 517747 values in range Counting number of voxels in first frame Found 517746 voxels in final mask Writing output to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter.nii.gz Count: 517746 517746.000000 16777216 3.086007 mri_binarize done mri_binarize --i /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 175 --o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter++.nii.gz 7.2.0 cwd /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer cmdline mri_binarize --i /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 175 --o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter++.nii.gz sysname Darwin hostname Ashwatis-Mac-Studio.local machine x86_64 user ashwativipin input /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_recons/BIOC_0001_v01_FS/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 13 0 2 1 41 2 7 3 46 4 172 5 177 6 77 7 28 8 60 9 16 10 173 11 174 12 175 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 MRIcopyHeader(): source has ctab Starting parallel 1 Found 546411 values in range Counting number of voxels in first frame Found 546410 voxels in final mask Writing output to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter++.nii.gz Count: 546410 546410.000000 16777216 3.256857 mri_binarize done mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/aparc+aseg.bbr.nii.gz mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/aparc+aseg.bbr.nii.gz reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -9.31323e-10) j_ras = (0, -1.15688e-08, -1) k_ras = (0, 1, -2.91038e-09) INFO: Reading transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99990 0.00494 0.01304 0.19200; -0.00511 0.98920 0.01758 -0.54272; -0.01259 -0.01741 0.99397 1.73988; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/aparc+aseg.bbr.nii.gz... mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/aparc+aseg_mask.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -9.31323e-10) j_ras = (0, -1.15688e-08, -1) k_ras = (0, 1, -2.91038e-09) INFO: Reading transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99990 0.00494 0.01304 0.19200; -0.00511 0.98920 0.01758 -0.54272; -0.01259 -0.01741 0.99397 1.73988; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz... mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/White-Matter.bbr.nii.gz mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/White-Matter.bbr.nii.gz reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -9.31323e-10) j_ras = (0, -1.15688e-08, -1) k_ras = (0, 1, -2.91038e-09) INFO: Reading transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99990 0.00494 0.01304 0.19200; -0.00511 0.98920 0.01758 -0.54272; -0.01259 -0.01741 0.99397 1.73988; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/White-Matter.bbr.nii.gz... mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter++.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/White-Matter++.bbr.nii.gz mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter++.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/White-Matter++.bbr.nii.gz reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/White-Matter++.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -9.31323e-10) j_ras = (0, -1.15688e-08, -1) k_ras = (0, 1, -2.91038e-09) INFO: Reading transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99990 0.00494 0.01304 0.19200; -0.00511 0.98920 0.01758 -0.54272; -0.01259 -0.01741 0.99397 1.73988; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/White-Matter++.bbr.nii.gz... fslstats -t /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi.nii.gz -k /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_snr.txt mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/lowb_brain_mask.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz mri_convert -at /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta -rt nearest /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/lowb_brain_mask.nii.gz /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz reading from /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/lowb_brain_mask.nii.gz... TR=3600.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, -0.000400775, -0.0245065) j_ras = (0.000400775, 0.999465, -0.0326939) k_ras = (-0.0245065, 0.0326939, 0.999165) INFO: Reading transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/xfms/diff2anatorig.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 1.87367 0.00823 0.14699 4.69244; 0.07013 0.02859 -3.91970 164.38367; -0.00920 1.89492 0.05850 1.30824; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz... #------------------------------------- #@# Tensor fit Tue Oct 18 17:30:21 +08 2022 dtifit -k /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/data.nii.gz -m /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/bvecs -b /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/bvals -o /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dtifit 0 128 0 128 0 36 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed #------------------------------------- #@# Inter-subject registration Tue Oct 18 17:30:26 +08 2022 set: Variable name must contain alphanumeric characters.