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>> 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>> 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> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> 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> >>>> 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 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.
