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 = (-0.999976, -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 > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
