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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
