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 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.
