Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in [mydata}/cope7ACroi_rh.osgm.rfx.
There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), and even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, gammavar, mask, and sig) but no rh.cope7.mgh. Thanks for going back and forth about this, Susan On Tue, 3 Nov 2015, Douglas N Greve wrote: > The correct command line is > > --cache 4 neg --cache-label AC > > On 11/03/2015 03:36 PM, s...@u.washington.edu wrote: >> Hi Doug, >> >> >> >> So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot >> find any documentation about what to put instead of --grf), as in >> >> mri_glmfit-sim --glmdir >> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx >> --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces >> >> I get back "ERROR: Flag 4 is unrecognized." >> >> If I try just --cache instead of --cache-label AC, I get back "ERROR: >> cannot find >> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh" >> >> Any thoughts? >> >> Many thanks, >> Susan >> >> On Tue, 3 Nov 2015, Douglas N Greve wrote: >> >>> The fwhm.dat file was in the right place. You passed the wrong folder to >>> mri_glmfit-sim. You should pass it >>> >>> cope7ACroi_rh.osgm.rfx >>> >>> doug >>> >>> >>> On 11/03/2015 02:40 PM, s...@u.washington.edu wrote: >>>> 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 >>>> >>>> >>> >>> -- >>> 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 >>> >> >> > > -- > 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
