Re: [Freesurfer] if: Expression Syntax

[Morenikeji Adebayo]

Hi Doug, fordoug2 is attached. Thanks, Keji

fordoug2.log
Description: Binary data

On Jul 24, 2015, at 11:17 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: can you run register-sess -debug -s nmasa_031_130412 -d /autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 -per-run -update |& tee fordoug2.log and send me fourdoug2.log doug On 7/24/15 10:22 AM, Morenikeji Adebayo wrote: Hi there, Attached is the log file from running: preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run |& tee fordoug.log I got more errors when I ran: preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per |& tee fordoug.log Thanks, Keji On Jul 23, 2015, at 6:05 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: Yes, but you have a typo -min305 instead of -mni305 On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote: I sure can. Hopefully. Is the what you need? On Jul 22, 2015, at 5:01 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: can you just send the log and not put it into a doc file? On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote: No problem! Here you go. On Jul 22, 2015, at 4:30 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: Sorry, there should not be a * at the end of -per. I was just trying to copy your command line with -debug as the first arg. On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote: Hi Doug, When I run: preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log I get: preproc-sess: No match. Thanks, Keji On Jul 22, 2015, at 3:37 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> wrote: * Can you run the following preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per* |& tee fordoug.log and send me fordoug.log On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote: Hi there, I’m running stable: source /usr/local/freesurfer/stable5_3_0 Thanks, Keji On Jul 21, 2015, at 4:56 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: what environment are you running in? ie, dev or stable? On 7/21/15 2:12 PM, Morenikeji Adebayo wrote: Hi there, *When running selxavg for the following session:* nmasa_031_130412 * * *The following error message was generated:* * * Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm (MRIread) Error in fast_selxavg3 (line 146)  runmask = MRIread(flac.maskfspec); * * *I did some investigating and discovered that all the bold runs for this participant are missing the following files:* * * .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz * * * So I ran: preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh -min305 -fwhm 5 -per * * * *Which generated the following error message:* if: _expression_ Syntax **Do you have any idea what might be going wrong with this subject or what this error message (**if: _expression_ Syntax) **means?** * * * * Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 <http://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu><mailto:k...@nmr.mgh.harvard.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 <http://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <http://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> <mailto:k...@nmr.mgh.harvard.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu <mailto:k...@nmr.mgh.harvard.edu> _______________________________________________ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu

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