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
<http://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
<http://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::exceptionLinux
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 2014For more details, see the log file
/tmp/14663415.qsched02.quest.it.northwestern.edu/GBM/20140728_132405/DN6741NMFF/FreeSurfer/DN6741NMFF/scripts/recon-all.log
<http://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
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>*
--
C. Paula de los Angeles, MD/PhD student
Medical Scientist Training Program
Northwestern University Feinberg School of Medicine
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