[Freesurfer] QC Montages error
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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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/ventz
[Freesurfer] QC Montages error
Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem. I probably gave more output than necessary. 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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 s
Re: [Freesurfer] QC Montages error
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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 `./0
Re: [Freesurfer] QC Montages error
Hi Chindhuri, I don't know anything about those scripts (I don't think that they are distributed with FS). Why are you using version 4? doug Chindhuri Selvadurai wrote: > Hello, I have tried troubleshooting this problem in various ways, but I am > still not able to figure out the problem. > > I probably gave more output than necessary. > > 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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 s
Re: [Freesurfer] QC Montages error
Hi Chindhuri, I don't think we have access to that path where the scripts are. Double-check the path names in your script, it looks like some of the path names are relative. Also, make sure you are running the script from the right directory to begin with. -Louis On Mon, 25 Jul 2011, Chindhuri Selvadurai wrote: > > Hello, I have tried troubleshooting this problem in various ways, but I am > still not able to figure out the problem. > > I probably gave more output than necessary. > > 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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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 = (-0.76, -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_
