Re: [Freesurfer] recon-all error
Yes, I ran it with the -i first, and I got this error: ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. I deleted all the files, and re-ran, and it still didn't work, so I then deleted the -i flag and tried again. In the log file, it says that you did not run it with the -i. Check your command line. doug Chindhuri Selvadurai wrote: Hello, I am having trouble doing a recon-all of my data. pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i /cluster/archive/295/siemens/TrioTim-35006-20111026-155248-065000/364000-15-01.dcm -mail chin...@nmr.mgh.harvard.edu' Here is the error: ERROR: no run data found in /autofs/cluster/manoach/dod/subjects/DODASD001/mri. Make sure to have a volume called 001.mgz in /autofs/cluster/manoach/dod/subjects/DODASD001/mri/orig. If you have a second run of data call it 002.mgz, etc. I usually do the recon all through launchpad first before any other preprocessing, and hadn't had a problem before? Not sure why this is the case this time. What step should be done before this to get the data in the mri? My subjects_dir is /cluster/manoach/dod/subjects Thanks so much! ___ 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 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 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.
[Freesurfer] recon-all error
Hello, I am having trouble doing a recon-all of my data. pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i /cluster/archive/295/siemens/TrioTim-35006-20111026-155248-065000/364000-15-01.dcm -mail chin...@nmr.mgh.harvard.edu' Here is the error: ERROR: no run data found in /autofs/cluster/manoach/dod/subjects/DODASD001/mri. Make sure to have a volume called 001.mgz in /autofs/cluster/manoach/dod/subjects/DODASD001/mri/orig. If you have a second run of data call it 002.mgz, etc. I usually do the recon all through launchpad first before any other preprocessing, and hadn't had a problem before? Not sure why this is the case this time. What step should be done before this to get the data in the mri? My subjects_dir is /cluster/manoach/dod/subjects Thanks so much! ___ 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.
Re: [Freesurfer] mri_glmfit .nii files
I am actually getting an error message when I type my mri_glmfit command: ERROR: fio_pushd: /group_analysis/volume/m1/mstmct_v_base/type_v_rest ERROR: must specify input y file I did specify a y file and I do not know what fio_pushd is. This is controlled by the $FSF_OUTPUT_FORMAT. By default this is compressed nifti (nii.gz). Both nii and nii.gz store the same information. The nii.gz is compressed, so you save some space. doug Chindhuri Selvadurai wrote: Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm Not sure why this is the case.. any help would be appreciated! Thanks! ___ 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 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 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.
[Freesurfer] mri_glmfit .nii files
Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm Not sure why this is the case.. any help would be appreciated! Thanks! ___ 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.
[Freesurfer] isxconcat-sess missing dof file
Hi all, When I run isxconcat-sess, I am experiencing an error finding a 'dof' file in my analysis directories within the FSD files. subjects directory: /cluster/manoach/milton/subjects command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c type_v_rest_vol -o /cluster/manoach/milton/subjects/group_analysis/volume/ output: /cluster/manoach/milton/subjects/group_analysis/volume//mstmct_v_base/log/isxconcat.log ERROR: cannot find /autofs/cluster/manoach/milton/subjects/PAMST02/bold/mstmct_v_base/dof Did I miss a step before the isxconcat? Thank you! ___ 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.
[Freesurfer] QC Montages error
/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 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.
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 `./013/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash:
[Freesurfer] preprocessing qc
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 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.
[Freesurfer] QC Montages error
/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 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.
Re: [Freesurfer] launchpad help
I thought the default was p10, so I just used that to try again, however I'm still getting that error with no extra info in the log. what is the name of the queue, maybe that is my problem: command: pbsubmit -q p10 -l nodes=1:opteron -m chinsel -c 'recon-all -s RMAUT021 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@nmr.mgh.harvard.edu -force' output: Opening pbsjob_4 qsub -V -S /bin/sh -m abe -M chinsel -q p10 -l nodes=1:opteron -r n /pbs/chinsel/pbsjob_4 qsub: Job exceeds queue resource limits MSG=cannot locate feasible nodes FATAL: qsub call failed. Check above for error messages. [1] + Done gedit pbsjob_3 What exact website page are you using for help on launchpad? launchpad has no opteron nodes so you should not be specifying that resource. Its queue names are also different than seychelles. There is no sergeant queue. Read: https://www.nmr.mgh.harvard.edu/martinos/itgroup/launchpad.html On Tue, 21 Jun 2011, Chindhuri Selvadurai wrote: Hello, I am trying to do recon-all using launchpad, and I am not sure how to fix the error I am getting. I checked IT's launchpad help website, but can't seem to figure it out. Using fs v4 subjects_dir: /space/ventzl/36/users/RespMon12C/subjects command: pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all -s RMAUT021 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@nmr.mgh.harvard.edu -force' This is the output I'm getting: Opening pbsjob_3 qsub -V -S /bin/sh -m abe -M chinsel -q sergeant -l nodes=1:opteron -r n /pbs/chinsel/pbsjob_3 qsub: Unknown queue MSG=cannot locate queue FATAL: qsub call failed. Check above for error messages. I'm also not getting any e-mails. Is there a way to check an error log like on seychelles? 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 --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 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 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.
[Freesurfer] launchpad help
Hello, I am trying to do recon-all using launchpad, and I am not sure how to fix the error I am getting. I checked IT's launchpad help website, but can't seem to figure it out. Using fs v4 subjects_dir: /space/ventzl/36/users/RespMon12C/subjects command: pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all -s RMAUT021 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@nmr.mgh.harvard.edu -force' This is the output I'm getting: Opening pbsjob_3 qsub -V -S /bin/sh -m abe -M chinsel -q sergeant -l nodes=1:opteron -r n /pbs/chinsel/pbsjob_3 qsub: Unknown queue MSG=cannot locate queue FATAL: qsub call failed. Check above for error messages. I'm also not getting any e-mails. Is there a way to check an error log like on seychelles? 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 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.
[Freesurfer] Error in recon-all on seychelles
Hello, I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem. I am using freesurfer 4, so I set this var before sourcing the script: setenv USE_STABLE_4_5_0 source /usr/local/freesurfer/stable4 My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been: /usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all -s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-04-01.dcm -mail chin...@nmr.mgh.harvard.edu -force' I would appreciate your help! Thank you, Chindhuri S Original Message Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From:adm a...@nmr.mgh.harvard.edu Date:Thu, June 2, 2011 2:03 pm To: chin...@nmr.mgh.harvard.edu -- PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01 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 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.
Re: [Freesurfer] Error in recon-all on seychelles
I'm not sure how to get that information. It does not give me an error message in the terminal. Is there a log I could look at? Is there anything that I need to do prior to the recon-all? Hi Chindhuri, we'll need to know what the error was that resulted in the non-zero exit status. cheers Bruce On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote: Hello, I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem. I am using freesurfer 4, so I set this var before sourcing the script: setenv USE_STABLE_4_5_0 source /usr/local/freesurfer/stable4 My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been: /usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all -s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-04-01.dcm -mail chin...@nmr.mgh.harvard.edu -force' I would appreciate your help! Thank you, Chindhuri S Original Message Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From:adm a...@nmr.mgh.harvard.edu Date:Thu, June 2, 2011 2:03 pm To: chin...@nmr.mgh.harvard.edu -- PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01 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 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 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.
Re: [Freesurfer] Segmentation Fault
Not happening anymore, thanks! Hi Chinduri, is this still happening? I can't replicate. doug Chindhuri Selvadurai wrote: Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command a while ago, and the command worked fine at that time. Do you have any idea what would be causing this error? The output is included below: Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 Subjects Dir: /cluster/manoach/milton/subjects FreeSurfer v. Stable 5 Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 Fri May 13 12:21:58 EDT 2011 Run: 012 Fri May 13 12:21:58 EDT 2011 Update not needed Fri May 13 12:21:58 EDT 2011 register-sess completed PBMCT15 MC - mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run -nolog -update Logfile is /dev/null --- /autofs/cluster/manoach/milton/subjects/PBMCT15 RunList: 012 --- ** --- --- Motion Correcting Run 012 --- --- ** --- sess = PBMCT15 Fri May 13 12:21:58 EDT 2011 mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat 012/fmcpr.mcdat /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii log file is 012/fmcpr.nii.gz.mclog mcdat file is 012/fmcpr.mcdat tmp dir is 012/tmp.mc-afni2.3377 #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from 012/template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998297, -0.0395807, 0.0428535) j_ras = (0.0411249, -0.998513, 0.0357732) k_ras = (0.0413739, 0.0374746, 0.998441) changing data type from short to float (noscale = 0)... writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float Segmentation fault Thanks! 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 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 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.
[Freesurfer] Segmentation Fault
Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command a while ago, and the command worked fine at that time. Do you have any idea what would be causing this error? The output is included below: Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 Subjects Dir: /cluster/manoach/milton/subjects FreeSurfer v. Stable 5 Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 Fri May 13 12:21:58 EDT 2011 Run: 012 Fri May 13 12:21:58 EDT 2011 Update not needed Fri May 13 12:21:58 EDT 2011 register-sess completed PBMCT15 MC - mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run -nolog -update Logfile is /dev/null --- /autofs/cluster/manoach/milton/subjects/PBMCT15 RunList: 012 --- ** --- --- Motion Correcting Run 012 --- --- ** --- sess = PBMCT15 Fri May 13 12:21:58 EDT 2011 mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat 012/fmcpr.mcdat /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii log file is 012/fmcpr.nii.gz.mclog mcdat file is 012/fmcpr.mcdat tmp dir is 012/tmp.mc-afni2.3377 #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from 012/template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998297, -0.0395807, 0.0428535) j_ras = (0.0411249, -0.998513, 0.0357732) k_ras = (0.0413739, 0.0374746, 0.998441) changing data type from short to float (noscale = 0)... writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float Segmentation fault Thanks! 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 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.
[Freesurfer] fs stable 4 vs 5; preproc-sess
Hello, We have a question about preprocessing in fs4 compared to fs5. We used the preproc-sess command without specifying -surface or volume and did all our processing and analysis in fs5. I believe in fs4 you didn't have to specify this. Do you think this is a problem for doing both surface and volume based analyses? Do you think it wise to redo the preprocessing? Let us know if you need more info. Subjects dir: /cluster/manoach/milton/subjects Command used: preproc-sess -s $subject -d /cluster/manoach/milton/subjects/ -per-run -fwhm 8 ___ 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.
Re: [Freesurfer] Abblocked Setup
Dear Doug, Thanks for your response! Our stimuli starts with the null condition, but abblocked assumes it's the ON condition. Is there a way to invert this? When we look at the sig maps, how do we know what the contrast is? Which condition does it think is null/task, negative/positive? From what I understand from your first e-mail, this is the opposite of what we want. I tried looking at the surface-based analysis using tksurfer, but since there is no constrast file for abblocked, I specified all contrasts, but how do you differentiate if you have more than one? tksurfer-sess -s PBMST08 -hemi -lh -analysis mandy_mst_v_mct_lh -call I think perhaps it would be better for us to switch to the block design to make things simpler? Thanks!! Chindhuri sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? 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 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 -- 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 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 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.
[Freesurfer] abblocked Setup
Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? 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 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.
Re: [Freesurfer] Abblocked Setup
Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? 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 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 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.
Re: [Freesurfer] spmregister error
package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg Two suggestions: 1. Can you temporarily change the spm path to spm5 to see if that fixes the problem? 2. Can you send me your command line, directory you ran it from, SUBJECTS_DIR, and terminal output? doug Chindhuri Selvadurai wrote: The path to spm2 was not originally in my startup.m file, but even when I added it, it didn't work. I am using 7.8, but I tried to change my cshrc file back to 7.1 however, once I ran the script, it was actually running 7.4 Thank you, Chindhuri Chindhuri, Is the path to spm2 added in your startup.m file and are you using matlab 7.1 (required by spm2)? doug Chindhuri Selvadurai wrote: Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@partners.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617)726-0307 -- 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 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617)726-0307 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617)726-0307 ___ 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.
Re: [Freesurfer] spmregister error
Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last row in the FreeSurfer FAST section, under the line beginning with clear. Hope that helps! -Adam Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed __ Our information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: purkinje SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons PWD: /cluster/ablood/1/DMRF_ASL ssh purkinje setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons cd /cluster/ablood/1/DMRF_ASL __ We appreciate any help you can give us!! Thanks, Sandra Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital 120 6th St. Charlestown, MA 02129 Tel: 617-643-6245 Fax: 617-726-1351 Email: swoodm...@partners.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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. * [Freesurfer] spmregister error swoodman o Re: [Freesurfer] spmregister error Adam Nitenson + Re: [Freesurfer] spmregister error Douglas N Greve # Re: [Freesurfer] spmregister error swoodman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
