It's: mri_glmfit --y /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh --osgm --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx --surf fsaverage lh --label /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for some other files needed and I moved them. Is the problem something in my mri_glmfit command? Susan On Tue, 3 Nov 2015, Douglas N Greve wrote: > > it cannot find this file > > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat > > which should have been created by mri_glmfit. What is your mri_glmfit > command line? > > Also, don't use --grf, that is for volumes only > > > On 11/03/2015 02:27 PM, s...@u.washington.edu wrote: >> Hi DOug, >> >> doug.log is attached >> >> the bash equivalent for |& is 2>&1 | >> >> thanks, >> Susan >> >> On Tue, 3 Nov 2015, Douglas N Greve wrote: >> >>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not >>> sure what the bash equivalent is. Maybe |2 instead of |& >>> perhaps some bash experts can weigh in >>> >>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote: >>>> Hi Doug, >>>> >>>> Do you mean: >>>> >>>> mri_glmfit-sim --debug --glmdir >>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm >>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee >>>> doug.log? >>>> >>>> When I tried running the same code with |& tee doug.log at the end, >>>> I kept getting: >>>> >>>> syntax error near unexpected token `&' >>>> >>>> Thanks, >>>> Susan >>>> >>>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>>> >>>>> Can you run >>>>> >>>>> mri_glmfit-sim --debug --glmdir [my data >>>>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg >>>>> --cwpvalthresh 0.05 --2space |& tee doug.log >>>>> >>>>> and send me doug.log? >>>>> >>>>> >>>>> >>>>> >>>>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote: >>>>>> Hi experts, >>>>>> >>>>>> I am having trouble performing a Monte Carlo correction using >>>>>> mri_glmfit-sim. >>>>>> >>>>>> My data were sampled to fsaverage and smoothed at fwhm 5, using >>>>>> mris_preproc. I then ran mri_glmfit on the data. >>>>>> >>>>>> I want to do my analysis/correction only in auditory cortex (AC) >>>>>> so I did my own simulation in AC of each hemisphere using >>>>>> mri_mcsim (as per >>>>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo). >>>>>> >>>>>> So far, so good. >>>>>> >>>>>> But when I try to run: >>>>>> >>>>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm >>>>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space >>>>>> >>>>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override >>>>>> 5, but it didn't help. >>>>>> >>>>>> Any thoughts? Also, can you clarify which comparison neg vs pos >>>>>> will give me? >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Susan McLaughlin, PhD >>>>>> Research Scientist >>>>>> Laboratory for Auditory Brain Sciences & Neuroengineering >>>>>> Institute for Learning & Brain Sciences (I-LABS) >>>>>> Portage Bay Bldg. Room 204 >>>>>> University of Washington, Box 357988 >>>>>> Seattle, WA 98195-7988 >>>>>> >>>>>> Ph: (206) 616-0102 Fx: (206) 221-6472 >>>>>> Cell: 206-850-8638 >>>>>> E-mail: s...@uw.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. >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >>> >> >> >> _______________________________________________ >> 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
