Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem.
Does anyone have any idea? Thank you! > I am getting an error when using a script that combines these 3 actions: > > preproc.sh > std_map_qc_montages.bash > put_tpef.bash > > > Freesurfer version 4 > SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects > Script: > /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh > > It looks like the preproc-sess finishes okay, but the problem starts > afterwards, but I'm not sure how to fix this easily.. it looks like it's > looking for files that aren't there, but I haven't gotten this error > before. > > Thanks! > > Output, with error at end: > > ----------------- mkbrainmask Done ----------------------------- > > Thu Jul 7 17:15:21 EDT 2011 > mkbrainmask-sess done > ---------------------------------------- > Started at Thu Jul 7 16:54:00 EDT 2011 > Ended at Thu Jul 7 17:15:21 EDT 2011 > preproc-sess done > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > mri_convert f.nii fskip8.nii --nskip 8 > nskip = 8 > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from f.nii... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.999976, -0.00683426, -0.00130865) > j_ras = (0.0069578, -0.984569, -0.174858) > k_ras = (-9.34106e-05, -0.174863, 0.984593) > Skipping 8 frames > writing to fskip8.nii... > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./011/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./011/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./011/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./013/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./013/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./013/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./015/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./015/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./015/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./017/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./017/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./017/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./019/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./019/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./019/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./021/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./021/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./021/lightboxes/tmean_lightbox.png': No such file or > directory > bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No > such file or directory > cp: cannot stat `./023/lightboxes/tsnr_lightbox.png': No such file or > directory > cp: cannot stat `./023/lightboxes/tstd_lightbox.png': No such file or > directory > cp: cannot stat `./023/lightboxes/tmean_lightbox.png': No such file or > directory > > Cannot open tsnr_lightbox1.png for reading > /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: > line 35: 28671 Segmentation fault pngappend tsnr_lightbox1.png + > $((gap)) tsnr_lightbox2.png + $((gap)) tsnr_lightbox3.png - $((gap)) > tsnr_lightbox4.png + $((gap)) tsnr_lightbox5.png + $((gap)) > tsnr_lightbox6.png tsnr_all.png > > Cannot open tstd_lightbox1.png for reading > /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: > line 36: 28672 Segmentation fault pngappend tstd_lightbox1.png + > $((gap)) tstd_lightbox2.png + $((gap)) tstd_lightbox3.png - $((gap)) > tstd_lightbox4.png + $((gap)) tstd_lightbox5.png + $((gap)) > tstd_lightbox6.png tstd_all.png > > Cannot open tmean_lightbox1.png for reading > /autofs/cluster/manoach/AS/RespMon12C/scripts/RM12C_lightbox_runs.bash: > line 37: 28673 Segmentation fault pngappend tmean_lightbox1.png + > $((gap)) tmean_lightbox2.png + $((gap)) tmean_lightbox3.png - $((gap)) > tmean_lightbox4.png + $((gap)) tmean_lightbox5.png + $((gap)) > tmean_lightbox6.png tmean_all.png > mv: cannot stat > `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/all_lightboxes/*all*': > No such file or directory > rm: cannot remove > `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/0*/lightboxes/': > No such file or directory > _______________________________________________ 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.
