You have to tell it not to do all the operations after the per-hemi phase. At one point, it used to be easy to do this, but I don't think anyone ever used the per-hemi operations and now it might not be possible. doug
On 07/29/2014 10:40 AM, C. Paula de los Angeles wrote:
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 http://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 http://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. http://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. http://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. http://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. http://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 http://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::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 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*
-- C. Paula de los Angeles, MD/PhD student Medical Scientist Training Program Northwestern University Feinberg School of Medicine
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