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
