Sept. 15. 2020 error notes:

autorecon1 errors:
(base) jameshartzell@Jamess-MacBook-Pro 2nd.test.course.steps % recon-all -s S6_HU0936_05_04_12 -i S6_HU0936_05_04_12.struc_U.nii.gz -autorecon1 
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
......

1) #--------------------------------------------
#@# Talairach Failure Detection Mon Sep 14 15:42:17 CEST 2020
/Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7838, pval=0.8469 >= threshold=0.0050)
\n awk -f /Users/jameshartzell/freesurfer/bin/extract_talairach_avi_QA.awk /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/transforms/talairach_avi.log \n
\n tal_QC_AZS /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/transforms/talairach_avi.log \n
TalAviQA: 0.98159
z-score: 0
#--------------------------------------------

2) ***********************************************
Computing MAP estimate using 3292 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.07656   0.05146   0.00419  -18.50909;
-0.04043   1.13887   0.19720  -18.33480;
 0.00433  -0.22750   0.99619   13.79424;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3292
Quasinewton: input matrix
 1.07656   0.05146   0.00419  -18.50909;
-0.04043   1.13887   0.19720  -18.33480;
 0.00433  -0.22750   0.99619   13.79424;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.07656   0.05146   0.00419  -18.50909;
-0.04043   1.13887   0.19720  -18.33480;
 0.00433  -0.22750   0.99619   13.79424;
 0.00000   0.00000   0.00000   1.00000;
 
3) **************************************************
 EM alignment process ...
 Computing final MAP estimate using 364986 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.07656   0.05146   0.00419  -18.50909;
-0.04043   1.13887   0.19720  -18.33480;
 0.00433  -0.22750   0.99619   13.79424;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364986
Quasinewton: input matrix
 1.07656   0.05146   0.00419  -18.50909;
-0.04043   1.13887   0.19720  -18.33480;
 0.00433  -0.22750   0.99619   13.79424;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) =    4.1  tol 0.000000
final transform:
 1.07656   0.05146   0.00419  -18.50909;
-0.04043   1.13887   0.19720  -18.33480;
 0.00433  -0.22750   0.99619   13.79424;
 0.00000   0.00000   0.00000   1.00000;
 
 end of autorecon1
 #@#%# recon-all-run-time-hours 0.417
recon-all -s S6_HU0936_05_04_12 finished without error at Mon Sep 14 16:03:04 CEST 2020

Autorecon2:
1) ***********************************************
Computing MAP estimate using 2841 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.10217  -0.00621  -0.01739  -12.56401;
 0.01026   1.15861   0.17326  -22.02631;
 0.01676  -0.19246   0.96909   13.19612;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2841
Quasinewton: input matrix
 1.10217  -0.00621  -0.01739  -12.56401;
 0.01026   1.15861   0.17326  -22.02631;
 0.01676  -0.19246   0.96909   13.19612;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.10217  -0.00621  -0.01739  -12.56401;
 0.01026   1.15861   0.17326  -22.02631;
 0.01676  -0.19246   0.96909   13.19612;
 0.00000   0.00000   0.00000   1.00000;
 
2) **************************************************
 EM alignment process ...
 Computing final MAP estimate using 315638 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.10217  -0.00621  -0.01739  -12.56401;
 0.01026   1.15861   0.17326  -22.02631;
 0.01676  -0.19246   0.96909   13.19612;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315638
Quasinewton: input matrix
 1.10217  -0.00621  -0.01739  -12.56401;
 0.01026   1.15861   0.17326  -22.02631;
 0.01676  -0.19246   0.96909   13.19612;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) =    3.8  tol 0.000000
final transform:
 1.10217  -0.00621  -0.01739  -12.56401;
 0.01026   1.15861   0.17326  -22.02631;
 0.01676  -0.19246   0.96909   13.19612;
 0.00000   0.00000   0.00000   1.00000;
 
 3) Presumably not a real problem?
 #--------------------------------------
#@# CC Seg Mon Sep 14 19:47:36 CEST 2020
\n mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/transforms/cc_up.lta S6_HU0936_05_04_12 \n
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/transforms/cc_up.lta
reading aseg from /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/aseg.auto_noCCseg.mgz
reading norm from /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/norm.mgz
22182 voxels in left wm, 42863 in right wm, xrange [125, 132]
searching rotation angles z=[-7  7], y=[-8  6]
searching scale 1 Z rot 6.5  global minimum found at slice 129.0, rotations (-1.24, -0.24)
final transformation (x=129.0, yr=-1.243, zr=-0.242):
 0.99976   0.00422  -0.02170   1.12128;
-0.00422   0.99999   0.00009   37.53428;
 0.02170   0.00000   0.99976   11.22781;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 91 114
eigenvectors:
-0.00038  -0.00336   0.99999;
-0.04305  -0.99907  -0.00337;
 0.99907  -0.04305   0.00023;
error in mid anterior detected - correcting...
error in mid anterior detected - correcting...
writing aseg with callosum to /Users/jameshartzell/freesurfer/subjects/S6_HU0936_05_04_12/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.2 minutes

4) NOTE: the following appeared in the terminal output at the end of autorecon3
#--------------------------------------------
#@# WhiteSurfs lh Tue Sep 15 09:26:08 CEST 2020
CBVfindFirstPeakD1: Undefined variable.