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 = (-0.999976, -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 >> > > > > > Best, > > Chindhuri Selvadurai > > Psychiatric Neuroimaging, Manoach Lab > Martinos Center for Biomedical Imaging, MGH > Phone: (617)726-0307 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list 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