Hi Freesurfer team,

I am running into an issue when I am specify the -hemi flag for the recon -all command (in this case recon -all -hemi rh). The command seems to work for the most part, except it errored at the end and seemed to be looking for a file for the other hemisphere. How do I get this command to work without exiting with errors? Is there an alternative set of commands that you recommend or something that I can add to ignore this step but still get the output that I need?   Thanks in advance for your help.

​See log output below (and let me know if you need more information from me to help me):

#@# Cortical Parc 3 rh Tue Jul 29 05:55:38 CDT 2014
/tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 DN6741NMFF rh ../surf/rh.sphere.reg /projects/p20394/software/freesurfer-v5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /projects/p20394/software/freesurfer-v5.3.0/average/rh.DKTatlas40.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.008
0 singular and 237 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1840 labels changed using aseg
relabeling using gibbs priors...
000:   2985 changed, 153010 examined...
001:    741 changed, 12861 examined...
002:    207 changed, 4026 examined...
003:     98 changed, 1267 examined...
004:     48 changed, 574 examined...
005:     17 changed, 275 examined...
006:     10 changed, 87 examined...
007:      8 changed, 58 examined...
008:      5 changed, 53 examined...
009:      3 changed, 29 examined...
010:      3 changed, 20 examined...
011:      4 changed, 17 examined...
012:      2 changed, 17 examined...
013:      0 changed, 13 examined...
200 labels changed using aseg
000: 131 total segments, 98 labels (1131 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 48 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
803 vertices marked for relabeling...
803 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 6 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Tue Jul 29 05:56:44 CDT 2014
/tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/scripts

 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab DN6741NMFF rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/mri/wm.mgz...
reading input surface /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/surf/rh.white...
reading input pial surface /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/surf/rh.pial...
reading input white surface /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/surf/rh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

 1734   1086   2805  2.403 0.674     0.235     0.238      118    16.1  caudalanteriorcingulate
 3720   2180   4531  2.150 0.629     0.245     0.364      522    54.9  caudalmiddlefrontal
 2021   1319   2928  2.047 0.780     0.290     0.395      159    41.7  cuneus
 1035    578   1950  2.643 0.868     0.283     0.593      113    25.1  entorhinal
 3294   2144   5529  2.550 0.826     0.261     0.323      355    33.0  fusiform
 8115   4699  12385  2.474 0.681     0.218     0.385     1067   111.9  inferiorparietal
 5792   3558  11712  2.670 0.824     0.258     0.651     1276    80.5  inferiortemporal
 1182    694   1693  2.338 0.774     0.235     0.286      111    10.8  isthmuscingulate
 8508   5665  10029  1.913 0.707     0.287     0.317      913    98.2  lateraloccipital
 4737   2826   8278  2.610 0.800     0.243     0.312      580    69.6  lateralorbitofrontal
 4163   2801   5096  1.844 0.654     0.323     0.712     1466    80.9  lingual
 2241   1422   4125  2.433 0.741     0.280     1.242      844    33.4  medialorbitofrontal
 6452   3907  13716  2.889 0.770     0.231     0.251      568    60.1  middletemporal
 1215    702   1834  2.439 0.696     0.215     0.276       84    13.3  parahippocampal
 2949   1703   2784  1.862 0.622     0.303     0.470      972    53.7  paracentral
 2339   1409   3508  2.338 0.507     0.222     0.404      180    32.0  parsopercularis
 1339    758   2560  2.812 0.683     0.252     0.325      143    15.7  parsorbitalis
 2072   1187   3544  2.675 0.574     0.213     0.238      230    26.1  parstriangularis
 1751   1204   1751  1.571 0.476     0.330     0.389      329    27.5  pericalcarine
 6976   4154   8485  1.915 0.698     0.215     0.212      560    65.5  postcentral
 2082   1283   2695  2.149 0.562     0.258     0.288      171    22.4  posteriorcingulate
 8338   5164   9837  1.901 0.590     0.249     0.295      848   109.7  precentral
 5984   3699   7924  2.173 0.596     0.272     0.408      950    79.8  precuneus
  956    553   1572  2.876 0.582     0.216     0.274       61    11.1  rostralanteriorcingulate
 8324   4521  10959  2.272 0.615     0.230     0.340     1301   122.1  rostralmiddlefrontal
19072  11009  25827  2.268 0.664     0.265     0.528     4152   282.6  superiorfrontal
 9478   5499  12173  2.169 0.589     0.230     0.323     1069   108.6  superiorparietal
 8064   4853  14648  2.618 0.807     0.249     0.505     1153   118.9  superiortemporal
 5940   3499   8741  2.426 0.605     0.210     0.346     1138    81.6  supramarginal
  723    669   1016  1.703 0.586     0.357     0.317      102     8.4  transversetemporal
 2944   1804   5524  3.067 0.820     0.251     0.310      203    33.4  insula
#--------------------------------------------
#@# Cortical ribbon mask Tue Jul 29 05:57:22 CDT 2014
/tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon DN6741NMFF

SUBJECTS_DIR is /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer
MRISread(/tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/surf/lh.white): could not open file
loading input data...
No such file or directory
 Exception caught while processing input files
std::exception
Linux qnode0621 2.6.32-358.7.1.el6.x86_64 #1 SMP Tue Apr 9 18:08:17 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s DN6741NMFF exited with ERRORS at Tue Jul 29 05:57:22 CDT 2014

For more details, see the log file /tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
​